Jossed: At the time there was a popular theory that the Mother Elf was originally a reploid (more specifically Iris from X4) based on the fact that X and Elpizo underwent a similar transformation. This theory was officially disproved in Complete Works where is stated that the Mother Elf was created from the Maverick Virus data in Zero's body.
The original X himself was going to be the Big Bad, and not just some copy. Presumably after having to deal with the maverick uprising all by himself for over a hundred years, he would have snapped and Jumped Off The Slippery Slope in the name of protecting humans. The Big Bad being a copy instead was literally a last month decision, and done because it was felt X being a canon Ron the Death Eater wouldn't sit well with the kids who played the X series games where he was the hero.
Ciel was originally drafted as a cyborg.
"Harpuia" was originally meant to be the name of the character's swords.
Zero 2: A bat-like One-Winged Angel form was planned for Phantom to match the other three Guardians', although considering that Phantom had already been killed off, it may have simply been drawn on a whim. See here.◊
Young, middle-aged, and elderly (i.e. the final version) designs were drafted for Weil. The young version had a Mini Mecha.
Omega's second form would have been much more active (for example, actually using its BFS) if not for GBA's graphics limitations.
The series was originally meant to end with the third game, with Dark Elf now free, X finally retiring into Cyberspace, and Omega being destroyed for good. Thankfully, they changed the Post Script Season that is Zero 4 into an epic Grand Finale (though with some Fridge Logics here and there).
The bad part about that: The 3rd game actually left a good hook for Mega Man ZX, which caused the for the most part happy ending of the 3rd game to be overridden and retconned the previous ending to kill 3 major characters offscreen.
Volteel Biblio's design is adapted from an older design for a electric eel boss.