>>33646376There's two Mewtwo in both the games and the anime. The first (the original from Kanto) is male and can't Megavolve. The second one was created by Team Plasma, was female in both movies she appeared in, and evolved into Mega Mewtwo Y - in the games, she shows up in Kalos in X/Y and drops her Megastone when captured/defeated, though which stone you get depends on the version.
As for why anyone would use Mega Y over regular Life Orb Mewtwo,
>>33643566 said it best. Besides, I actually like how Y's design makes it look closer to Mew.
