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Morbi
The way I see it, Gamefreak only brought back Mewtwo to lure in the older generation of Pokemon players back into the game, same reason they only gave the Gen1 starters a Mega-Evo. I really don't see them using him again from this point on, and since Gamefreak influences pokemon additions to smash I doubt they would push for him all that much.
As far as popularity goes, Charizard beats Mewtwo hands down. In this regard I think Charizard takes the cake for Pokemon included due to popularity.
People always bring up the fact that Mewtwo was planned before, but at the end of the day the fact that matters is that he didn't make it in. For some reason or another Sakurai always puts him in the back of the production line. Which to me seems to be an indicator that he doesn't much care for him. Also if they (Sakurai, Gamefreak and Nintendo) thought that Mewtwo would be such a big copy seller in regards to the Smash franchise, they would've prioritized him in Brawl.
For me, the final nail in the Poke-coffin was the greninja trailer. Greninja's charge attack was an obvious misdirection intended to make people think it was Mewtwo, and it worked; just look at all the reaction videos on youtube as people clamor for Mewtwo before being surprised.
Look, I'm not anti-Mewtwo. I would be very glad to see him in the game (especially instead of Lucario), but I just don't think he's as likely as people hype him up to be.