What makes you think MewTwo will be coming back? Gen1 already has Pikachu and Jigglypuff.
I don't think anyone (sans super Pokémon fanboys who will buy the game anyways) really cares about which generation a Pokémon is from, so long as they are popular and would make for an awesome playable character.
As for Mewtwo, he has been the most requested character that wasn't in Brawl since Brawl launched, and it hasn't even been close.
Mega Man was from what I can gather the most requested potential newcomer for Smash 4.
There was a huge difference is how many people wanted Mewtwo compared to Mega Man.
Now that Mega Man's in, and K. Rool, Ridley, Little Mac, and Miis are the top potential newcomers, yeah, Mewtwo's odds look even greater.
On top of that, the manner in which Mewtwo was cut (probably for Sonic to join the roster in 2007) suggests that his reappearance is yet again very likely.
Popularity, which I honestly think is hilarious. Wasn't he the subject of many jokes before people found out he was cut?
We thought it was the dumbest idea, because fixing him could be done in so many ways.
And it was one of the definitively dumb decisions Sakurai, Game Arts, and Sora did in Brawl.