Mewtwo being an artificial pokemon, how can it mega Evolve? Has the mechanics of Mewtwo mega Evolution been explained in the Genesect movie, game or any other canon?
It's only theoretical and the evidence may not me be true to the games, but in the first movie we see Mewtwo create new Pokeballs, that can even capture a Pokeball, and the pokemon once captured going through DNA engineering device to be cloned, so it's not too far to say that Mewtwo is the one who created the Mega Stones for him.
Although the theory might not well combined with the game, I can bring reference to that from the game, once captured in Pokemon X\Y the player is given automatically the Mewtwonite as shown it was where Mewtwo is found, it may imply that Mewtwo already had the Mewtwonite.
Though in the remakes for Sapphire and Ruby the player finds the mega stone for Mewtwo in the Pokemon League buildings, still it's only theory.
(all this support @kaine comment)