In a recent edition of his column for Famitsu (as reported by Polygon), Super Smash Bros. director Masahiro Sakurai explained his reasoning behind his choices for new challengers Villager, Wii Fit Trainer, and Mega Man for the upcoming Wii U and Nintendo 3DS fighting games. He points out that Villager was actually a consideration for Super Smash Bros. Brawl, only to be cut, and that "Something I think that people noticed in the movies and screenshots released is that the villager and trainer were not choices we made for the sake of cheap novelty," pointing out the unique attributes they bring to the game.
As for Mega Man, he wrote:
For Mega Man as well, if all we cared about was who we could get in the game, then he would just have regular old punches and kicks, like how he largely does in the Marvel vs. Capcom series. But Mega Man's most unique trait is how he gains new attacks from bosses. Working that fully into the game results in a more complete Mega Man that we can give you. That's why he's done up in NES-era proportions rather than something more realistic; that's why he's a little expressionless; that's why his jumping and damage motions and the way he can fire the Mega Buster while walking are all what they are. It's all in an effort to present the character.
Making a game by yourself is one thing, but if a lot of people are involved, retaining a unified direction is vital. Every member of the team has their own vision of Mega Man that springs to mind instantly when they think about it. However, as long as the original image you construct remains firm, then that can survive a few discrepancies without the character falling apart. So what's key in character selection is whether the guy dances out at you, and whether you have what it takes to portray that appeal.
For what it's worth, we think that they've portrayed Mega Man's appeal quite stunningly, and that he's going to not only dance out at people, but all over a lot of video game faces, too.