I'd more prefer it if most of Mewtwo's specials got altered...
standard - Aura Sphere: Mewtwo will charge up an energy orb, which gains power the longer it's held. Mega Mewtwo Y's version is stronger in power, but doesn't travel as far.
side - Psycho Cut: Mewtwo fires blades made of psychic energy that it can charge up. Mega Mewtwo Y's version is stronger, along with having a larger hitbox, but it doesn't travel as far.
up - Teleport: Same as in Melee. Mega Mewtwo Y's version creates an explosion upon reappearing, giving it some offensive purposes.
down - Mega Evolution: Mewtwo changes into Mega Mewtwo Y. If Mega Mewtwo Y uses this move, it'll revert back to its original state.
Final Smash - Psystrike: Mewtwo releases an odd power which damages all within its attack range. Mega Mewtwo Y's version is more powerful, but its attack range is much shorter.