Someone points that this thing is subtly explained in Origins.
You know, the Megastones were created years ago by the fuck up from the ultimate weapon and that shit. Mewtwo wouldn't have Megastones assuming this.
Fuji works on the Mewtwo proyect, and since in Origins at one point they mentioned Kalos, and the fact that Fuji hands the Megastone of Charizard to Red, it's the main point.
Fuji while working on Mewtwo, also researched about Megaevolution, thus creating the Megastones of Mewtwo and also another one, for the Pokémon of Giovanni as a kid, that's why Charizard X looks so different from regular Charizard while Y is more related.
This said, is just speculation, head canon, and if you want, made up bullshit. But I like this idea.
