The ever popular Mega Man series almost never made it off the ground. After creating the original Rockman game, creator Keiji Inafune and his staff knew they had something great on their hands. However Capcom almost wouldn't listen to their idea for Rockman 2. After some persuading, they were allowed to make the game as long as they finished the one they were assigned on time (a baseball game).

Rockman/Mega Man X5 was actually supposed to be the end of the X series, but Capcom went behind Keiji Inafune's back (more or less) and make X6 while Inafune made Rockman/Mega Man Zero. The two groups have come to a compromise as of late, using Rockman/Mega Man X8 and Rockman/Mega Man Zero 3 to close some of the plotholes left behind by this move.

Our beloved crimson Hunter, Zero, was originally not supposed to be revived after X1 (or X5, for that matter, but nevermind). He was originally supposed to just die, allowing X to have the drive to defeat Sigma he needed. However many Rockman fans, and Keiji Inafune himself, didn't like this idea and Zero was revived. (Keiji Inafune has remarked in recent interviews that Zero is one of his favorite characters too)

Wily has a pet bird named Reggae. He only appears in one or two games (most notably for Mega Man fans in Mega Man 7 when you get a password wrong). Unknown where he is in...pretty much every game aside from those.

All I can think of right now. I know a lot of Rockman/Mega Man stuff.