Theories about Mega Pokemon
With the Aerodactyl thing, one theory I came up with:
Mega Evolution is a thing similar to natural evolution, but the process is highly sped up.
For Pokemon with two Mega Evolutions, it could be something where there are 2 different paths a Pokemon could take, and each Mega Stone they have represents the different paths they can take. In the case of Mewtwo (since it was man-made and therefore may not be capable of natural evolution) the Mega Stones could originally have been different upgrades for Mewtwo which were then found and put into Mega Stones, allowing Mewtwo to be capable of Mega Evolution.