It also starred in M16 as the anime's first Mega Evolution, Origins as Red's final adversary, and obtainable legendary in X / Y.
I also wonder if it would get a revamped moveset like Bowser, especially after seeing it in action in Origins.
If Bowser can now run without looking awkward, I wonder if Mewtwo's running animation (trying to avoid M-Zard X's Swift) would be implemented.
As for specials, I don't mind Melee Mewtwo's but would love an overhaul based on its most recent appearances. Based off Origin's I would like
Neutral B: Either Recover (used vs. Articuno) and acting similar to P:M Lucas's Offense Up, Ivysaur's Solarbeam (healing portion) or WFT's Neutral B though self-healing moves can be an issue and probably avoided. Maybe Psycho Cut or whatever move was used to counterattack Articuno as a quick projectile. Though... I am fine with Shadow Ball.
Side-B: Could be Psycho Cut as previously mentioned or Telekinesis, a quick push that moves players / objects away from Mewtwo and can be used as a reflector.
Up-B: Teleport, no reason to change it.
Down-B: Barrier, which I think could be based on Mewtwo's defending attack when Charizard went for a Slash and work similarly to Mr. G&W's Oil Panic, where the Barrier would change color based on the number of times hit and unleash a powerful counterattack when completely filled up.
Final Smash: Psystrike. Mewtwo Mega Evolves into Mega Mewtwo Y to amplify the power of its attack, probably based on M16 (which I haven't watched).