...No.
HELL NO
If we get EXE representation it needs to be Bass.EXE. No Protoman because there's Zero already, and no Mega Man because I think another Rock would fit Marvel better. If you don't want to have two X representatives just make him his Zero version.
Other than some problems with character selection, I don't think you're ideas are too bad though.
If I had to choose the Megaman representatives for each series, it'd be like this (note, I'm not saying all of them should be in at the same time):
OG: Roll or Protoman
X: Zero with MMZ alt
Legends: Tron
BN: Bass.EXE
ZX: Ashe because Vent/Aile would just be Zero again :|
SF: Subaru/Geo and War-Rock/Mega (his power comes from bonds with other people, Marvel is a team game, how is he not fitting for the game? Make the Brother Band a mechanic for him.)
And Wily should be a boss character if only so that after you beat his first phase, he starts apologizing, but then suddenly...