I am currently rewatching B5 and recently read a book which covered DS9 and a bit of the B5 similarities as well.
Thus I feel confident to update the old thread a bit or add some more thoughts. Changes and updates in Bold.
So according to TVTropes, JMS had pitched Babylon 5 to Paramount (who turned it down) a year before they announced DS9. JMS then claimed for years that Paramount stole his story treatment, but he has since backed down after internal company memos came to light that showed the idea circulating around before he pitched his show. However, quite obviously the producers of DS9 took some inspiration from JMS original draft, hence the similarities between the two shows. (Ironically, the first draft of B5 from 1986 is a lot more closer to the finished TV show then the 1993 outline JMS used to sell the show to FOX, which was significantly watered-down to appease the network, pushing all the most expensive stuff into a hypothetical sequel series in order to sell them on the first one - so he probably tried to sell Paramount the show based on this first draft, which looked to expensive for Paramount...)
Let's say the producers decide to take JMS on board and merge their idea for DS9 with JMS outline.
How would such a DS9 look like?
The good thing is, JMS had a 5year story arc in mind, so DS9 doesn't loose 2 seasons to find its way (and no second pilot and reboot for season 4 is needed), albeit the Paramount guys might stretch that a little further than 5 seasons.
Plotwise, both shows a simliar enough that the Dominion (probably in its orignal for imagined as an anti-Federation) can stand in for the Shadows. The peoples JMS invented and their ambassadors, respectively would be changed to peoples we already know in the Star Trek universe. This could mean we see Klingons, Romulans, Cardassians, Ferengi instead of Narn, Centauri, Vorlons and Minbari guys as main characters for the show. Instead of a Narn-Centauri War, we probably see something like the Klingon-Cardassian War earlier in the series (maybe with Cardassia getting occupied). The infiltration of the Federation might lead to some greater problems than in OTL DS9 (like the original idea for "Homefront" and "Paradise Lost" as a finale for Season 3 and season 4 opening, with StarFleet ships firing on each other and causing a "near"-civil war) somewhat like the Earth Civil War in B5, thus Starfleet is unprepared when the Dominion (Shadows) attacks and the DS9/B5 crew has to look for other allies (like the Rangers in B5, the Army of Light respectively).
The main difference in the settings between DS9 and B5 is that the former is a Federation station (albeit shared with the Bajorans) guarding a wormhole (thus getting new aliens quick to the station every episode), while the latter is a explicitely a station for diplomacy (and commerce) located in neutral territory (albeit crewed by the Earth Alliance but co-sponsored by the Minbari). But me thinks that could be easily merged. In this case, we see permanent alien characters as ambassadors on the station.
The crew:
Characterwise, JMS planned for every major character a backdoor, in case an actor would drop out of the series (which proved very wise, see Sinclair/Sheridan and Talia/Lyta). This might lead to more changes in the cast during the series (in OTL DS9 we just got Word as an additional main character and Terry Farrel leaving at the end of season 6, so Dax got one additional host for the last season).
StarFleet Officers:
Sisko / Sinclair (interestingly, Richard Dean Anderson was considered for the role of Benjamin Sisko! As well as Siddig El Fadil - Bashir)
open questions if a Sheridan-like character has to be introduced at some point
Kira / Ivanova (this does not need to be a Bajoran, if they feature in this ATL show at all!)
Fun fact: Michelle Forbes, playing the part of Ensign Ro, was supposed to be Deep Space Nine's first officer, but Forbes didn't want to commit to a full television series - maybe the backdoor idea of JMS could convince her otherwise? Interestingly, Forbes was also approached for Voyager later on, which could lead to an ATL Worf (switching shows) here.
Doctor Bashir / Franklin - well obviously we here get the minority character, but a Bashir with drug problems could get more manifold
Security Chief Odo (?) or Garibaldi/Zack vs Eddington - frankly, I just can't see Odo fitting in here, he might better fit in as an mysterious alien ambassador or something, or he replaces the Eddington guy later on (if he becomes a traitor like in OTL DS9)
Tech Guy Miles O'Brien - well this is the one stock character we get to carry the torch from TNG, JMS would not protest me thinks
I noticed that some of the character traits of Garibaldi fit with O'Brien.
Alien ambassadors:
Klingon / Minbari - that's difficult to say, though later on it could be Martok (as in OTL DS9)
Cardassian / Centauri - well that's easy, plain old Dukat, according to rumor, the showrunners considered making Gul Dukat a member of the main cast. Alaimo was all for it, naturally.
Romulan / Narn - thinking that Andreas Katsulas played Tomalak, we might get a comeback of another TNG character here
Ferengi /? - Quark, who else? Interestingly, his OTL DS9 character was closest to being an ambassador (he becomes one in the relaunch novels)
As for the Vorlons - i don't really know, the closest we have to them in DS9 are the wormhole aliens and they have Sisko as their emissary...maybe Odo could be the guy in touch with them here.
Shadows / Mr. Morden - Weyoun, of course
Bester and the Psi Corps - Sloan and Section 31
B5 had some more characters added in the later run, such as Ranger Marcus Cole (only introduced in Season 3), which do not seem to have any equivalents in the DS9 universe (naturally as this happend as the show progressed and were not part of the original outline). DS9 got Worf in Season 4 though.
Furthermore, all alien ambassadors do have some aide – Londo has Vir Cotto, Delenn has Lennier and G'Kar had (at least in the first 2 seasons) Na'Toth and later Talon (for a while).
DS9 on the other hand developed other recurring characters later on, such as Eddington, Weyoun, Damar or Martok or Admiral Ross which became major characters (though not main characters) very late into its run. Not to forget Garak, of course which happend to be there frome the beginning (but was originally write as an one Episode character).
I notice that some of the character (stereo)types are corresponding to each other such as Londo as an annyoing guy who is usually at the butt of jokes (and having a naive aide) to Quark and Rom - though Londo does take a much darker path then Quark ever would (becoming the Dukat of B5 for a while) however he is in a way redeemed (as again compared to Dukat who just evolves from a morally ambigous villain to plain evil guy). Famously the quarrels of Quark and Odo and the quarrels of Londo and G'Kar, respectively. Some of the aides character types are similar to some of the minor DS9 characters, such as Lennier and Jake Sisko or a bit of Nog.
Suprisingly, a lot of developments in both shows had some similarities, like both Captains (Sisko was still a Commander then, though) getting a ship (Defiant / White Star) in the beginning of Season 3. The overall theme of a mighty thread lurking in the shadows (Dominion / Shadows) was also present for a while in both shows during the earlier seasons - before being revealed (JMS planned this from the very beginning though it is more obvious in Season 2, the audience however knows a lot more than the characters in the show, as we see the Shadow Ships from their first appearance in Signs and Portents in Season 1.) For DS9 however this holds true only for a part of Season 2 before the Season Finale reveals the Jem H'dar and the Season 3 Opener the Founders of the Dominion.
JMS seemed to have 2 major plot arcs planned for his show. The main arc with the "ancient enemy", the Shadows, who threaten humans and all other (major and minor alike) alien races, who first are plotting behind the scenes (which involves Londo mainly) and later are (slowly) revealed and strike openly against all who oppose them (or just stand in the way) which culminates in a big war and epic finale. Originally planned for a 5 year arc, the Shadow War arc would have been running longer (at least until the End of Season 4) but got cut short when B5 seemed not getting prolonged for a 5th Season (which it ultimately did). Thus JMS had to cramp the solution of the second arc into Season 4 as well. The main arc theme explains nicely why JMS considered Londo the main protagonist of the show.
The other major plot arc revolved around the Psi Corps and the human (mundanes) and telepath struggles, the so called Telepath (Civil) War. This never came really to fruition (and was extend in books) so JMS postponed the "war" aspect of it and adapted part of it into a much more simple Earth Civil War plotline which run concurrenty with the Shadow War plot (and got its conclusion in the latter half of Season 4). It seems that the original idea was that the Psi Corps was all along the way behind the ursupation of the Earth Government (by President Clark) and turning it into a dictatorship and the cooperation with the Shadows. Maybe this seemed to be too similar to the main plot (and the Psi Corps behaving like the Centauri).
However it did have major consequences for the main arc in the end (in Season 3 and 4), as Sheridan and the B5 crew are deprieved of support from home and the humans are NOT fighting against the shadows (as likewise the Centauri) thus the need for another "Army" the Rangers and the support of "minor" races to form the Army of Light and battle the Shadows. This contradicts a bit earlier episodes were it seemed that the humans are especially important to fight against the Shadows (compare Signs and Portents Season 1 again).
DS9 on the other hand developed the Dominion arc after a while into its run (in Season 2 and 3 to be precise) only to abandon it again for a while (though a Klingon intermezzo) in Season 4 and the first half of Season 5. Only then a major longer arc with a war was developed for the second half of Season 5 and first half of Season 6. Originally, the writers wanted the the war to end after the first 6 epsiodes but prolonged it after the "stalemate" in Sacrifice of Angels. Ultimately it was concluded only in the series finale.
The other main plot was about religion and beliefs - the "mystery" arc (so popular in the early 90s), which obviously was never very popular with the writers and the audience of the show. The "Bajoran religion" exploration episodes in the earlier Seasons (and the following tensions with the Starfleet staff) are at least controversial even among die hard fans of the show - however in the later Seasons this developed into Prophets versus Evil Prophets episodes which fit better into the overall narrative of the show (though still are controversial). This plot arc was also developed over the course of the show (e.g. the Evil Pagh Wraiths were originally just a side comment as a joke from a character when first mentioned) as there was no longterm planning when DS9 started.
Another minor recurring arc was the Maquis plot introduced in Season 2, but this was only used occasionally (mainly in Season 4 and 5) and with ony recurring character (Eddington) and turned rather into a strange vendetta (by Sisko). The feeling prevails that this whole storyline was forced on DS9 to have some overlap with TNG (and to bring Ro Laren into the cast, which did not happen) and later Voyager (were it felt totally unimportant). It was quickly abandoned and wrapped up in Season 5 before the Dominion War became hot.
The biggest similarity to JMS Earth Civil war storyline would be the DS9 two parter Homefront and Paradise Lost in Season 4. Interestingly this plot was developed as a cliffhanger for the end of Season 3 and the beginning of Season 4. It was postponed since the producers did not like it and wanted to introduce something to "shake things up", so Season 4 got instead the Klingons going on a rampage in the Opener Way of the Warrior (and the main cast got Worf as a backup). Interestingly JMS also used a 2 parter (Point of No Return and Severed Dreams) for a change in the series, but the whole arc started way earlier and ended much later.
The big difference is as in the B5 universe the coup against the civilian Earth Government succeeds, it fails in DS9 though both military characters fail - in this case played by the same actor (General Hague fails to prevent or counter the coup and Admiral Leighton fails to coup).
Taking under consideration that JMS planned the main arcs for a 5 Year run ahead but changed and adapted a lot of it during the shows run (ultimately under the duress of the show being canceled every season and actors having to be replaced) thus creating some minor inconsistencies, I can't see why he would not be able to do the same if he gets his idea adapted into the Star Trek Universe.
For him it might even work better if he does not have the stress that the show might be canceled before the main arc concludes, so the pace and overall feeling will probably be more like Season 1 of B5, a bit slower and with more filler episodes.
The main arc(s) needed Season 2-4 in B5 (though originally planned rather for 2-5), whereas DS9 needed 3-7 (albeit Season 4 is a bit of a sidestep, so it cames up one Season shorter). This means a minimum of 3-4 years B5 and 4-5 years of DS9 in comparison. Reasonably similar timewise, as DS9 contained an awful lot more of filler episodes anyway.
So which story parts could be combined for a B5 and DS9 transformation? And what could be omitted?
My opinion would be that much of the Shadow plotline could be transformed into the Dominion plot, since both are very similar anyway. JMS does have to drop the "mystery" plot around them a bit (being some of the First Ones and technologically 1000years ahead, representing chaos itself).
The Dominion could still be very well an "ancient" enemy though (Weyon stated that it is 10,000 years old and the Jem H'dar serve since 2000 years as frontline troops) - which could be the reason why the Wormhole was closed by the Prophets in the past. Especially if the original idea of an "anti-Federation" is maintained, the behaviour of the Shadows in recruiting allies (Drakh, Centauri) is copied in a way (though the Cardassians joining the Dominion is already like the Centauri striking deals with the Shadows). The main difference is while the Shadows represent Chaos (and the Vorlons Order), the Founders represent Order (albeit a very harsh version through oppression). Some of the alien races (Bajorans, Klingons, Cardassians) could have some memories of a war with the Dominion thousand(s) of years ago.
The other storyline or main arcs are a bit harder to merge. Especially since even JMS changed this over the course of B5s run, so a lot has to evolve during such a B5/DS9 hybrid shows run. I do see the possibility though, that some of the Psi Corps / Earth Civil War plot is switched to the Maquis and Earth Coup stories and ultimately the Section 31 plot. A lot of the Sisko and the Prophets stuff can be adapted by JMS since it is alike the Sheridan and the Vorlons stuff.
Weyoun can be more like a trader (then a diplomat like Morden) selling weapons and other things (drugs) to some of the alien governments through their "ambassadors". A secret rearment by the Cardassians, the thread of changelings infiltrating governments, a war of the Klingons and the Cardassians developing into a stalemate and again Weyoun promising to help for a prize. Thus ultimately a lot of alien races are weakend (Klingons, Romulans, Cardassians) and some are compelled to sign deals with the common enemy (Dukat). Sounds familiar like the shadows and the Narn Centauri war (if it would stalemate)?
Sisko would have to lobby harder to get an alliance to fight back and the Dominion would prove more overwhelming in the beginning of the war (planet killers, anyone?). Sisko would also need the help of the Prophets a bit more (aka Lorien and the First Ones) to turn the tide against the darkness.
Thus I feel confident to update the old thread a bit or add some more thoughts. Changes and updates in Bold.
So according to TVTropes, JMS had pitched Babylon 5 to Paramount (who turned it down) a year before they announced DS9. JMS then claimed for years that Paramount stole his story treatment, but he has since backed down after internal company memos came to light that showed the idea circulating around before he pitched his show. However, quite obviously the producers of DS9 took some inspiration from JMS original draft, hence the similarities between the two shows. (Ironically, the first draft of B5 from 1986 is a lot more closer to the finished TV show then the 1993 outline JMS used to sell the show to FOX, which was significantly watered-down to appease the network, pushing all the most expensive stuff into a hypothetical sequel series in order to sell them on the first one - so he probably tried to sell Paramount the show based on this first draft, which looked to expensive for Paramount...)
Let's say the producers decide to take JMS on board and merge their idea for DS9 with JMS outline.
How would such a DS9 look like?
The good thing is, JMS had a 5year story arc in mind, so DS9 doesn't loose 2 seasons to find its way (and no second pilot and reboot for season 4 is needed), albeit the Paramount guys might stretch that a little further than 5 seasons.
Plotwise, both shows a simliar enough that the Dominion (probably in its orignal for imagined as an anti-Federation) can stand in for the Shadows. The peoples JMS invented and their ambassadors, respectively would be changed to peoples we already know in the Star Trek universe. This could mean we see Klingons, Romulans, Cardassians, Ferengi instead of Narn, Centauri, Vorlons and Minbari guys as main characters for the show. Instead of a Narn-Centauri War, we probably see something like the Klingon-Cardassian War earlier in the series (maybe with Cardassia getting occupied). The infiltration of the Federation might lead to some greater problems than in OTL DS9 (like the original idea for "Homefront" and "Paradise Lost" as a finale for Season 3 and season 4 opening, with StarFleet ships firing on each other and causing a "near"-civil war) somewhat like the Earth Civil War in B5, thus Starfleet is unprepared when the Dominion (Shadows) attacks and the DS9/B5 crew has to look for other allies (like the Rangers in B5, the Army of Light respectively).
The main difference in the settings between DS9 and B5 is that the former is a Federation station (albeit shared with the Bajorans) guarding a wormhole (thus getting new aliens quick to the station every episode), while the latter is a explicitely a station for diplomacy (and commerce) located in neutral territory (albeit crewed by the Earth Alliance but co-sponsored by the Minbari). But me thinks that could be easily merged. In this case, we see permanent alien characters as ambassadors on the station.
The crew:
Characterwise, JMS planned for every major character a backdoor, in case an actor would drop out of the series (which proved very wise, see Sinclair/Sheridan and Talia/Lyta). This might lead to more changes in the cast during the series (in OTL DS9 we just got Word as an additional main character and Terry Farrel leaving at the end of season 6, so Dax got one additional host for the last season).
StarFleet Officers:
Sisko / Sinclair (interestingly, Richard Dean Anderson was considered for the role of Benjamin Sisko! As well as Siddig El Fadil - Bashir)
open questions if a Sheridan-like character has to be introduced at some point
Kira / Ivanova (this does not need to be a Bajoran, if they feature in this ATL show at all!)
Fun fact: Michelle Forbes, playing the part of Ensign Ro, was supposed to be Deep Space Nine's first officer, but Forbes didn't want to commit to a full television series - maybe the backdoor idea of JMS could convince her otherwise? Interestingly, Forbes was also approached for Voyager later on, which could lead to an ATL Worf (switching shows) here.
Doctor Bashir / Franklin - well obviously we here get the minority character, but a Bashir with drug problems could get more manifold
Security Chief Odo (?) or Garibaldi/Zack vs Eddington - frankly, I just can't see Odo fitting in here, he might better fit in as an mysterious alien ambassador or something, or he replaces the Eddington guy later on (if he becomes a traitor like in OTL DS9)
Tech Guy Miles O'Brien - well this is the one stock character we get to carry the torch from TNG, JMS would not protest me thinks
I noticed that some of the character traits of Garibaldi fit with O'Brien.
Alien ambassadors:
Klingon / Minbari - that's difficult to say, though later on it could be Martok (as in OTL DS9)
Cardassian / Centauri - well that's easy, plain old Dukat, according to rumor, the showrunners considered making Gul Dukat a member of the main cast. Alaimo was all for it, naturally.
Romulan / Narn - thinking that Andreas Katsulas played Tomalak, we might get a comeback of another TNG character here
Ferengi /? - Quark, who else? Interestingly, his OTL DS9 character was closest to being an ambassador (he becomes one in the relaunch novels)
As for the Vorlons - i don't really know, the closest we have to them in DS9 are the wormhole aliens and they have Sisko as their emissary...maybe Odo could be the guy in touch with them here.
Shadows / Mr. Morden - Weyoun, of course
Bester and the Psi Corps - Sloan and Section 31
B5 had some more characters added in the later run, such as Ranger Marcus Cole (only introduced in Season 3), which do not seem to have any equivalents in the DS9 universe (naturally as this happend as the show progressed and were not part of the original outline). DS9 got Worf in Season 4 though.
Furthermore, all alien ambassadors do have some aide – Londo has Vir Cotto, Delenn has Lennier and G'Kar had (at least in the first 2 seasons) Na'Toth and later Talon (for a while).
DS9 on the other hand developed other recurring characters later on, such as Eddington, Weyoun, Damar or Martok or Admiral Ross which became major characters (though not main characters) very late into its run. Not to forget Garak, of course which happend to be there frome the beginning (but was originally write as an one Episode character).
I notice that some of the character (stereo)types are corresponding to each other such as Londo as an annyoing guy who is usually at the butt of jokes (and having a naive aide) to Quark and Rom - though Londo does take a much darker path then Quark ever would (becoming the Dukat of B5 for a while) however he is in a way redeemed (as again compared to Dukat who just evolves from a morally ambigous villain to plain evil guy). Famously the quarrels of Quark and Odo and the quarrels of Londo and G'Kar, respectively. Some of the aides character types are similar to some of the minor DS9 characters, such as Lennier and Jake Sisko or a bit of Nog.
Suprisingly, a lot of developments in both shows had some similarities, like both Captains (Sisko was still a Commander then, though) getting a ship (Defiant / White Star) in the beginning of Season 3. The overall theme of a mighty thread lurking in the shadows (Dominion / Shadows) was also present for a while in both shows during the earlier seasons - before being revealed (JMS planned this from the very beginning though it is more obvious in Season 2, the audience however knows a lot more than the characters in the show, as we see the Shadow Ships from their first appearance in Signs and Portents in Season 1.) For DS9 however this holds true only for a part of Season 2 before the Season Finale reveals the Jem H'dar and the Season 3 Opener the Founders of the Dominion.
JMS seemed to have 2 major plot arcs planned for his show. The main arc with the "ancient enemy", the Shadows, who threaten humans and all other (major and minor alike) alien races, who first are plotting behind the scenes (which involves Londo mainly) and later are (slowly) revealed and strike openly against all who oppose them (or just stand in the way) which culminates in a big war and epic finale. Originally planned for a 5 year arc, the Shadow War arc would have been running longer (at least until the End of Season 4) but got cut short when B5 seemed not getting prolonged for a 5th Season (which it ultimately did). Thus JMS had to cramp the solution of the second arc into Season 4 as well. The main arc theme explains nicely why JMS considered Londo the main protagonist of the show.
The other major plot arc revolved around the Psi Corps and the human (mundanes) and telepath struggles, the so called Telepath (Civil) War. This never came really to fruition (and was extend in books) so JMS postponed the "war" aspect of it and adapted part of it into a much more simple Earth Civil War plotline which run concurrenty with the Shadow War plot (and got its conclusion in the latter half of Season 4). It seems that the original idea was that the Psi Corps was all along the way behind the ursupation of the Earth Government (by President Clark) and turning it into a dictatorship and the cooperation with the Shadows. Maybe this seemed to be too similar to the main plot (and the Psi Corps behaving like the Centauri).
However it did have major consequences for the main arc in the end (in Season 3 and 4), as Sheridan and the B5 crew are deprieved of support from home and the humans are NOT fighting against the shadows (as likewise the Centauri) thus the need for another "Army" the Rangers and the support of "minor" races to form the Army of Light and battle the Shadows. This contradicts a bit earlier episodes were it seemed that the humans are especially important to fight against the Shadows (compare Signs and Portents Season 1 again).
DS9 on the other hand developed the Dominion arc after a while into its run (in Season 2 and 3 to be precise) only to abandon it again for a while (though a Klingon intermezzo) in Season 4 and the first half of Season 5. Only then a major longer arc with a war was developed for the second half of Season 5 and first half of Season 6. Originally, the writers wanted the the war to end after the first 6 epsiodes but prolonged it after the "stalemate" in Sacrifice of Angels. Ultimately it was concluded only in the series finale.
The other main plot was about religion and beliefs - the "mystery" arc (so popular in the early 90s), which obviously was never very popular with the writers and the audience of the show. The "Bajoran religion" exploration episodes in the earlier Seasons (and the following tensions with the Starfleet staff) are at least controversial even among die hard fans of the show - however in the later Seasons this developed into Prophets versus Evil Prophets episodes which fit better into the overall narrative of the show (though still are controversial). This plot arc was also developed over the course of the show (e.g. the Evil Pagh Wraiths were originally just a side comment as a joke from a character when first mentioned) as there was no longterm planning when DS9 started.
Another minor recurring arc was the Maquis plot introduced in Season 2, but this was only used occasionally (mainly in Season 4 and 5) and with ony recurring character (Eddington) and turned rather into a strange vendetta (by Sisko). The feeling prevails that this whole storyline was forced on DS9 to have some overlap with TNG (and to bring Ro Laren into the cast, which did not happen) and later Voyager (were it felt totally unimportant). It was quickly abandoned and wrapped up in Season 5 before the Dominion War became hot.
The biggest similarity to JMS Earth Civil war storyline would be the DS9 two parter Homefront and Paradise Lost in Season 4. Interestingly this plot was developed as a cliffhanger for the end of Season 3 and the beginning of Season 4. It was postponed since the producers did not like it and wanted to introduce something to "shake things up", so Season 4 got instead the Klingons going on a rampage in the Opener Way of the Warrior (and the main cast got Worf as a backup). Interestingly JMS also used a 2 parter (Point of No Return and Severed Dreams) for a change in the series, but the whole arc started way earlier and ended much later.
The big difference is as in the B5 universe the coup against the civilian Earth Government succeeds, it fails in DS9 though both military characters fail - in this case played by the same actor (General Hague fails to prevent or counter the coup and Admiral Leighton fails to coup).
Taking under consideration that JMS planned the main arcs for a 5 Year run ahead but changed and adapted a lot of it during the shows run (ultimately under the duress of the show being canceled every season and actors having to be replaced) thus creating some minor inconsistencies, I can't see why he would not be able to do the same if he gets his idea adapted into the Star Trek Universe.
For him it might even work better if he does not have the stress that the show might be canceled before the main arc concludes, so the pace and overall feeling will probably be more like Season 1 of B5, a bit slower and with more filler episodes.
The main arc(s) needed Season 2-4 in B5 (though originally planned rather for 2-5), whereas DS9 needed 3-7 (albeit Season 4 is a bit of a sidestep, so it cames up one Season shorter). This means a minimum of 3-4 years B5 and 4-5 years of DS9 in comparison. Reasonably similar timewise, as DS9 contained an awful lot more of filler episodes anyway.
So which story parts could be combined for a B5 and DS9 transformation? And what could be omitted?
My opinion would be that much of the Shadow plotline could be transformed into the Dominion plot, since both are very similar anyway. JMS does have to drop the "mystery" plot around them a bit (being some of the First Ones and technologically 1000years ahead, representing chaos itself).
The Dominion could still be very well an "ancient" enemy though (Weyon stated that it is 10,000 years old and the Jem H'dar serve since 2000 years as frontline troops) - which could be the reason why the Wormhole was closed by the Prophets in the past. Especially if the original idea of an "anti-Federation" is maintained, the behaviour of the Shadows in recruiting allies (Drakh, Centauri) is copied in a way (though the Cardassians joining the Dominion is already like the Centauri striking deals with the Shadows). The main difference is while the Shadows represent Chaos (and the Vorlons Order), the Founders represent Order (albeit a very harsh version through oppression). Some of the alien races (Bajorans, Klingons, Cardassians) could have some memories of a war with the Dominion thousand(s) of years ago.
The other storyline or main arcs are a bit harder to merge. Especially since even JMS changed this over the course of B5s run, so a lot has to evolve during such a B5/DS9 hybrid shows run. I do see the possibility though, that some of the Psi Corps / Earth Civil War plot is switched to the Maquis and Earth Coup stories and ultimately the Section 31 plot. A lot of the Sisko and the Prophets stuff can be adapted by JMS since it is alike the Sheridan and the Vorlons stuff.
Weyoun can be more like a trader (then a diplomat like Morden) selling weapons and other things (drugs) to some of the alien governments through their "ambassadors". A secret rearment by the Cardassians, the thread of changelings infiltrating governments, a war of the Klingons and the Cardassians developing into a stalemate and again Weyoun promising to help for a prize. Thus ultimately a lot of alien races are weakend (Klingons, Romulans, Cardassians) and some are compelled to sign deals with the common enemy (Dukat). Sounds familiar like the shadows and the Narn Centauri war (if it would stalemate)?
Sisko would have to lobby harder to get an alliance to fight back and the Dominion would prove more overwhelming in the beginning of the war (planet killers, anyone?). Sisko would also need the help of the Prophets a bit more (aka Lorien and the First Ones) to turn the tide against the darkness.
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