there wasn't anything against Mewtwo's return, he didn't come back in Brawl.
And look how that turned out.
He's now the most requested character for the game.
Also, he was cut for time constraints (even Roy and Dr. Mario were too, despite actually having things against them). Do you honestly expect time constraints to cut content from a game that is releasing before almost everybody expected it to?
9/10 said Fall or Winter. And we're getting it in the Summer. Yet Brawl had a messy development with late content added on and got it's release pushed back many times. A lot of this was for the Subspace Emissary, which isn't happening again.
I see no reason. Cutting characters to cut characters will only make people mad, you don't see avid supporters for not having a certain character from Brawl to return... usually.