>>23396484Well fuck it's likely head-cannon but here's what I heard going around about both of those things.
Multiple Mewtwos: In the intro to the Genesect movie isn;t a lab scene shown where a couple of scientists are messing with a new Metwo in a tank? Either int he movie or an episode aired around that time. I'm pretty sure that one was Fem-Two, escaping like the last Mewtwo because fuck lab procedures. I think that explains Fem-Two's slightly different view on Pokemon and humans, and it got the Y form.
As far as it having mega stones from the reasons I've heard it's the same reason Charizard has two megas. In Origins the Charzardite X is fucking huge, and Charizard X looks completely unnatural for a mega evolution unlike charizard Y. I guess the theory goes team rocket used science and shit to artificially create Mewtwo's mega stones, and tested the principle on Charizard. Thats why Charizardite X is fucking huge compared to other stones and why I guess multiple variations of a mega were created for Mewtwo, to bring out it's power in any way needed.
Pic related, in the anime all the mega stones seen are about as big as the keystone.