Of course Mewtwo is returning. Every Pokemon is returning. He's not going to have an important role though.
And whatever the reasons were that they were cut do matter, because they could effect them again. The fact that people want them back may be a factor that can get them in, but people would have wanted them before Brawl came out, but something caused them to get cut. Its true that unless Sakurai actually says something about it, we will never know the truth, but whatever those reasons were, they are important to this, and could lead to insight as to how other characters could potentially be cut.
And it is close to a congress no matter how much you want to deny it. Characters who best represent a series are the characters who get in, and the FE and Pokemon series in particular seem to have a focus on two certain parts, the first and the latest. For Pokemon we already have more than enough characters representing the first games, so its best to give a new character spot to someone who's recent.
@Shortie: The notion that Lucario replaced Mewtwo and Ike replaced Roy is very very faulty, especially if you believe that both happened for the same reasons. If Lucario replaced anyone, it was Pichu, since that would make sense as the latest generation Pokemon. Mewtwo was almost certainly replaced by Pokemon Trainer, who was a out of left field character from gen 1. Either way, Mewtwo was planned at the same time that Lucario was planned, (same applies to Roy and Ike) so that also shoots down the "replaced" theory. Its actually likely though that Mewtwo was probably competing with a spot as the last Pokemon rep against Jigglypuff, as Jiggs is clearly a very late addition, while Mewtwo can be seen as the character who was last cut and farthest down in development.
In otherwords it was probably supposed to be [Pikachu, Jigglypuff, Mewtwo, Lucario] but someone came up with PT and it became [Pikachu, PT, Lucario, ???] and it took a bit of time for the team to decide of Jigglypuff rather than Mewtwo.