Marvel vs. Capcom 3, huh? I can dig it. I spent many a quarter on the prequels in my day. Fingers crossed for Moon Knight.
Anyhow, I agree with Zack here that they should make one gameplay mode that has all the fighters at the power level they traditionally possess. Of course it would make everything completely unbalanced (who could beat the Hulk?), but it would settle a lot of "who would win in a fight" forum disputes.
In this case, Magneto versus Megaman. Master of magnetism versus... a robot. I conjure the match would be quick.