Frankly I think the only reason why mewtwo couldn't be in this game will be due to a very serious bug or glitch, but probably since brawl they have already figured out how to do him.
I mean, Sakurai thinks mewtwo is relevant (made into melee as an original character, considered for both 64 and brawl, and cut only dueto technical stuff)
Pokemon fans consider mewtwo relevant, being the second most popular pokemon below charizard. with apeal to both casual and competitive players (mewtwo was probably one of the 3 most threatening pokemon in uber 5th gen, only below Arceus and Kyogre(haven't played 6th gen ubers))
Game freak considers mewtwo relevant, wasn'tconcidence than he got 2 megaevolutions, (Only shared with charizard) a new amazing signature move on 5th gen, and another movie.
Smash fanbase consider him relevant, probably the most wanted character in west and dunno how it is in japan, but i'm sure he is also VERY popular there, plus project M.
So frankly we can say that mewtwo IS very relevant to smash.