Well, to be fair, Mewtwo Returns implied it would take years to make another Mewtwo if the one they currently captured died under their care (Giovanni obviously didn't care since he wanted Mewtwo to suffer as revenge for his earlier rebellion), if they are even able to at all. Besides, whose to say they didn't? That Mewtwo special that led up to the Genesect Movie mentioned that the Mewtwo of that movie got created by some group earlier. Could easily be Team Rocket who was responsible in some way. And you have to admit, given all the data Giovanni would have had on Mewtwo relating to research and development, I'm pretty sure he would have at the very least deduced he had at least some involvement in any R&D on it even with his memory wipe.
As far as the first movie, in all fairness, it would have been difficult trying to do that for the intended age bracket. They'd need to rate it PG for it to fly, maybe even as high as PG-13.