If DS9 is treated more as a "TNG Sequel" instead of a spinoff, then I'd think it could get away with it being set on a space station (especially if the main characters had a ship from the beginning and DS9 is treated as a base of operations by the cast).
I could go along with this, to a point. Given DS9 is treated like a Starbase (& a transit hub in any event), there'd be ships (especially Starfleet ships, but also Bajoran, Cardassian, Andorian, Vulcan, even Klingon, Romulan, & Orion--& anybody else you want
) going thru the wormhole all the time. If you want/need a "ship story", use one of
those.
Having a Starfleet ship (not
Defiant, given the mission before the war starts) permanently attached makes sense; making her a
Miranda, say, with her CO a senior Lt, & a regular member of the cast (or regular guest star, as Garak was), works nicely: DS9 is her base of operations, & we get to know her CO (& her crew!) as recurring guest starts--without the stupidity of Sisko & Co abandoning
their stations.
I'd also keep the high number of Bajorans, which were around in the first season (or two?), but dispensed with, later: it's still Bajoran property, after all. Indeed, I'd flip the relationship between Sisko & Kira:
she is in charge. (Unless there's a dynamic I've forgotten that persuaded Bajor to give over command to Sisko--& it would have to be
compelling.)
In that vein, I liked the tension between Kira & Sisko in the beginning, & I'd keep it; there's no reason they have to end up besties. (If Bajor is Israel & UFP is the U.S., tension is sometimes going to happen...
)
Finally, I'd keep "nasty Quark", as he was in the pilot (& in the flashback stories). He was much more interesting that way, & a much more credible opponent to Odo (& Sisko/Kira). (He'd also make Ferengi seem actually dangerous, which the writers kept undermining with stories making them out as complete clowns.
)
Edit to add...
One other thing. I'd use different Cardassians for some of the stories the writers used Dukat for. He was vain & self-important, but by the time they were done, they'd turned him into an insane clown that was just preposterous from a character standpoint. That doesn't help the character or the show at all.
Edit 2 to add:
I'm kinda wishing Q gets butterflied
He would be. TTL, Gene isn't in (likely to be) in charge, & therefore can't rewrite Dorothy's screenplay for "Farpoint", introducing Q.
Would Deanna Troi be a Doctor then? That would be a logical choice given her OTL position as a counselor.
I'd far rather she was a kind of Protocol Officer, as implied in the pilot, rather than senior ship's psychiatrist. When introduced, I had the sense she was Hayden to Picard's Michael:
consigliere.
Edit to add 3:
The only real problem I had with DS9 was turning the Klingons into "Space Vikings" and going all-in on the warrior aspect.
I actually found that interesting--in part because we almost never see Klingons who
aren't warriors. (You'd have to have a UFP character live among Klingons for that.)
If there's one thing I feel like I do especially well ITTL is I make the Klingons rational actors in all my stories.
You did that well, IMO. None of them is doing something bad just because the story needs a bad guy.
The other thing I would have changed about DS9 (although this could have been a budget thing IRL) is I would have shown more of the Gamma Quadrant once the Dominion was being built up as the big bad. I think 98% of the action was in the Alpha Quadrant or with the Bajoran spirits in the wormhole. DS9 (and maybe even Voyager ITTL?) could explore the Alpha Quadrant.
I suspect it's a budget issue. More aliens means more actors & more appliances, & more unique sets, & (arguably) more ship miniatures. (Recall, "DS9" wasn't using CGI, and miniatures are
costly.
)
That said, I suspect lack of imagination played a part...
Star Trek JAG and Star Trek West Wing are interesting concepts; I get a little bit into the politics within the Federation and Klingon Empire (and a little of the Romulans too) in Starfleet Intelligence...
Starfleet not having a JAG was pure stupidity (or writer ignorance). And there were several episodes in the franchise offering opportunities for spinning it off, all the way back to "Court Martial".
Your treatment of the politics in "SI" is the "dirty" side (or the covert); "UFP West Wing" would show the process leading to (& reasons for needing) an "SI" team being sent in.
I almost want to treat the wormhole like a galactic Suez Canal with the Federation, Cardassians and Dominion all interested in the "galactic chokepoint". DS9 and the wormhole are agreed to as neutral space after the Cardassians are thrown off Bajor, but the Federation, Cardassians and Dominion are all angling for full control.
That was my sense of the situation in-show.
betrays Cardassia and double-crosses the Federation by "claiming" the wormhole.
I don't see a doublecross, exactly, but a Cardassian claim would probably provoke a war anyhow--Bajor would certainly object. (Indeed, Bajor, as Egypt in this scenario, has the best claim for ownership.)