The only Pokémon with multiple mega evolutions are Charizard and Mewtwo. In Pokémon Origins, Red is given a key stone and a Charizard mega stone by Mr. Fuji, who was also said to have a hand in creating Mewtwo. Do you think there might be some sort of connection?
Ehh… honestly… no, not really. If that was supposed to be a significant detail, I think Origins probably would have found a way to show one of Mewtwo’s mega evolutions. I don’t really see anything there that rises above the level of coincidence.