>>30989936Mewtwo is a clone of Mew.
Since Mew's DNA is too complex to create a perfect clone, Mewtwo is always the result of said cloning.
In some continuities (Namely both the long running Shopro anime, and Pokemon SPecial Manga), Team Rocket was involved in the monster's creation seeing that it could help them with their poaching schemes. Because of this, it have a mistrust towards humans.
As for the MegaStones and Z-crystals, just assume that those were mere coincidences.