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.
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 Dr. Cain and other civilians are killed in the Sky Lagoon crash. Alia, Signas, Douglas and possibly Dynamo are introduced a game early. Ends on a bittersweet note, as Sigma crashes the Final Weapon into Earth, despite X and Zero's efforts.
Mega Man X5: A combination of OTL's X5 and X6; Capcom puts all their eggs into one basket and releases a much better game in 2001. Gate attempts to discredit the Maverick Hunters after the Earth's destruction through his own Reploids and uses the Nightmare to play into X and Zero's guilt; the latter especially, as visions of Iris and other Repliforce members appear (replacing Zero Nightmare). Thanks to Isoc, Zero succumbs to the Nightmare Virus and finally goes Maverick, though he recovers after X destroys the Nightmare Mother, which Gate fuses with for the final boss.
Mega Man X7: Red Alert are the antagonists and aren't controlled by Sigma. Zero is retired after the last game, due to his guilt, but eventually springs back into action. X briefly leads the Maverick Hunters and is willing to take Axl onboard, acting as a mentor figure to him. This would technically be X6, meaning X8 would be X7 and so on, but whatever.
Mega Man Xtreme 3: A filler game of sorts that gives Axl some character development and delves into his origins. The villain can be Sigma or someone else entirely (in the former's case, I think it makes sense for Axl to encounter him before the next game).
Mega Man X8: Dynamo replaces Vile and Dr. Wily's return is hinted at; I'm tempted to remove Palette and maybe Layer in favour of Douglas coming back, but I know both are fan favourites, so I'm not sure about that. Everything else, otherwise, is the same as before.
Mega Man X9: The last mainline X game and longest too, with ten Mavericks and a second set of final stages. Lumine takes control of Axl and continues his uprising; Dynamo replaces him as the third playable character. Sigma returns once more, but isn't permanently defeated, as the virus still lingers. The series culminates in a final battle against Dr. Wily.
Offscreen, before the events of Z1, Zero submits himself to science, while Axl is kept away in solitary confinement, with remnants of Lumine still lingering within. When the Elf Wars break out, Axl has his mind taken out or erased, but not before shapeshifting into a new body for Zero; this is based on a TV Tropes WMG I read a while back.
Command Mission: Still takes place in its own timeline, parallel to the Zero series. With a few more chapters, the plot would be more fleshed out and characters like Marino and Cinnamon would have more to do. 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.
Mega Man X Dive: A fun, non-canon crossover with the other Mega Man series, essentially a redo of X-Over.
