Gonna drop some story changes for the Mega Man X series. I'm far from a good writer, so feel free to tear this apart.
Mega Man X1: Effectively unchanged, other than giving X more than one line of dialogue.
Mega Man X2: The Japanese script is intact (including the references to Dr. Wily) and Fake Zero gets a boss fight.
Mega Man X3: Dr. Doppler is the final boss, the Nightmare Police is cut or has more to do and Iris makes an earlier appearance as a navigator; Repliforce themselves are foreshadowed in some way, so that their presence in the next game doesn't come out of nowhere.
Mega Man Xtreme: Is set after X3 instead of before it; Mac is the antagonist instead of Sigma.
Mega Man Xtreme 2: Sigma isn't revealed as the twist villain; Gareth replaces him as the final boss.
Mega Man X4: A three-way war between the Hunters, Repliforce and Mavericks breaks out after Double, under the orders of "an old scientist guy", crashes the Sky Lagoon; Dr. Cain is among the civilians killed, dealing a bigger blow to Repliforce's name. X is given his own subplot, where he goes after Dragoon (the main suspect of the crash) and struggles to fight some of his former friends; at some point, he discovers the teammates that were killed by Double. X and Zero regroup for the final story and take on Iris, General and Double. The Final Weapon is shut down.
Mega Man X5: Opens with Dynamo uploading the Maverick Virus onto the Final Weapon's computer, allowing Sigma to take control and lead it on a collision course with Earth. Although X and Zero defeat him again, they fail to stop the Final Weapon from crashing into the planet. X vs Zero is removed and saved for a later game. Signas, Alia, Douglas and Lifesaver are also given proper introductions.
Mega Man X6: The Maverick Hunters' reputation has been damaged after failing to save the Earth. The effects of the Nightmare would be more devastating, with environments warping, visions of Iris and other dead Reploids, etc; Alia also
becomes corrupted by the Nightmare Souls. Gate and Isoc, due to conflicting interests and ideals, begin to fall out as the game progresses; instead of reviving Sigma, Gate tries to take control the Nightmare Mother, only for it to turn him into a zombified monster. The post-apocalyptic theme is carried over into the sequels.
Alternatively, Gate survives and the final boss could be Sigma still (revived by Isoc instead) or someone else, like the Nightmare Mother alone or High Max. I heard the devs wanted to keep him around and it would give room to flesh out his character and backstory. He would stick around as a recurring antagonist before finally being killed off in X8 or X9.
Mega Man X7: Red and his teammates are acting on their own will instead of being controlled by Sigma. X rescues Axl and is willing to take him onboard, rather than being retired or overly pacifistic. Dr. Light's sentience isn't retconned. Axl is revealed later on
to have been created by Gate (whether he actually encounters him or not).
Mega Man X8: The character designs from X6 and X7 are kept. Vile and, perhaps controversially, Palette and Layer are cut for the returns of Dynamo and Douglas, as well as a new character, a Reploid scientist named Alfred (later revealed to be Dr. Wily), respectively. If played on easy mode, Lumine is still fought, but dies before he can unleash Paradise Lost; this ending would lead into Command Mission. On normal and hard difficulties, however, Lumine misses Axl and accidentally strikes Zero instead.
Mega Man X9: Like X4, each character has their own story; X goes after the possessed Zero, Axl begins to learn of his origins and Dynamo is still on the run after the last game. After Zero is defeated, Alfred captures and reprograms him. X, Axl and Dynamo's paths converge and they team up to stop him. Awakened Zero is the penultimate boss, followed by a final showdown against Alfred/Wily.
Once he's defeated, Wily's AI form is released; as he curses them, Dr. Light suddenly appears. He has a deep conversation with Wily, reflecting on their past and revealing the respect he had for him deep down, despite everything that's happened, as well as reminding him that their time is long gone and they've overstayed their welcomes. Wily is moved by this and accepts his fate, as both fizzle away, having finally found closure. (This last idea is based on a comment I saw on Reddit, so credit where it's due.)
After X9, Zero partially regains control over his body and is submitted to science, since the Virus originated from him. Following some experiments, a mixture of his own DNA and Lumine's is reverse engineered to create the Mother Elf. Once the Elf Wars roll around, Axl voluntarily has his mind removed in order to provide Zero with a new body, but not before shapeshifting into the one seen in the Zero series (you could explain his decision by having him be wounded in battle or something).
Command Mission: Still takes place in an alternate timeline, parallel to the Zero series; Wily, Sigma, Weil, etc would have been dealt with offscreen. With a few more chapters, the plot would be more fleshed out and characters like Marino and Cinnamon would have more screen time. The cliffhanger ending is followed through in a sequel.
Maverick Hunter X: Is a retelling of the first game with extra details added, rather than a continuity reboot; this would apply to a hypothetical Maverick Hunter X2 and so on. Vile's campaign is replaced by a Zero mode, where he fails to save X in time and has to fight the Mavericks alone.
