>>18853555I said this in the a headcanon thread a few weeks ago and in a mewtwo thread after that, but I'll say it again, so beware, headcanon ahoy
Mr Fuji was working on the Mew project and had a hand in its creation. Origins showed how Mr Fuji knew about Mega Stones (which makes sense since he has worked with scientists around the globe, probably including Kalos). It's totally possible, given those two things that he created Mewtwo (made from Mew, a being containing the DNA of ALL Pokémon) specifically to react to the two Mega Stones. This also fits in with his reputation as the strongest Pokémon ever, since he was specifically designed to be as close to perfect as possible AND to Mega Evolve into 2 forms!
But if we're going with a super simple, less cool explanation:
>>18853854>>18855071I'd agree, but if that were the case, no character would refer to it as Mewtwoite X or Y, it'd just be Mewtwoite or whatever