Like pokemonfan794 said, the 'original' Mewtwo also appears in another film alongside all of the clones he created. without spoiling too much of the movie, Mewtwo grows to trust humans more and agreed to let Brock, Misty, and Ash to keep their memories that time as long as they promised to never speak of the incident or himself and his fellow clones. In the Genesect film, Ash acts a certain way upon seeing this other Mewtwo. Its almost as if he knows the pokemon itself but also has feeling its a different one entirely, he also remembers the promise he made so he doesn't say anything about it.
Due to Ash, Brock, and Misty being the only ones aware of the first ones existence, it's highly possible Giovanni attempted the experiment again only to fail from the same mistake, for even his memory was erased in Mewtwo Returns by Mewtwo. Other mad scientists could have tried to create a copy of mew as well, any existing records of the first were destroyed after all.
I know this may be a late response, but this is important to think about as well.