You have to remember Mewtwo is not 100% artificial. It is a clone of Mew with scientifically implanted genetics. Mega Stones are just a result of a meteor crashing down on the Pokemon World and there could have been a stone for Mew, but instead there was a stone for Mewtwo
I don't mean to sound rude, but I honestly think you should ask the Pokémon Company if you wanna know that bad. None of us know the answer to this question because it is not us who invented mega mewtwo.