I'm not against it per se, but if I personally had to choose it would go to Classic Mega Man, Mega Man X, Proto Man, or Zero. Hell even Sigma, or Vile. (Villains need some showings too.)
To me as along time gamer, those 4 represent the Mega Man series far better than .EXE. I haven't honestly played any of the new Mega Man games, because they differ soo much form the old platforming style the older games had. I mean I'd take .EXE simply because he would be a new character, and I love new characters. BUT Mega Man/MMX hold a much deeper place in my heart than Lan, and .EXE.
It may be true his hands turn into other things, but what makes you think Nintendo can't use boss moves form the original games, and X, for his smash attacks?
I'll think on it a bit, and come back with some potential smash attacks, that could be used from the old Mega Man games and X games.