I'm one of those that would want X to instead of classic Megaman. But let's face it, it's makes more sense that X isn't in the game. I think that the classic version fits better in with the rest characters, and it would be wrong to have X since it was the classic Megaman who started everything in the first place. It's just logical.
As for the "cloning problem", I can't speak for brawl, but the difference between the clone and the original becomes more apparent the more you play with those characters. And quite frankly, they are very different in the way you play with them. Even if the attacks looks the same, they do different things. In my mind at least, that's enough to seperate them. That being said, they sure could use some more unique attacks.
Finally I would like to see the return of Mewtwo. It made no sense removing him from Brawl. He is, I think, one of the most original characters in melee. He feels so different to control from everyone else and is one of the more interesting characters to play in that game. And if the reason was because he sucked, well you got plenty of those characters in the game.
Of the top of my head: Kirby, Bowser, Donkey Kong, Pickachu, Ness, Game & Watch, Roy, Yoshi, Zelda.
And I get it, several of those are well established characters and everyone would rage if they were removed. I'm just saying.
EDIT: Btw, Wii Fit Trainer. Am I the only one who thinks that's strange?