I usually avoid taking this road given the mixed behavior of Mewtwo (including my own for personal reasons). I'll use the Japanese animated since it was the anime that first imbued Myuutsu with a personality.
Anti-hero is the main convention and with Myuutsu's later reactions, I'll concede that, but I want to focus on his origin here. Don't forget, he had trust in humans originally (Birth of Myuutsu short/CD Drama) with Ai-Two, but he couldn't grapple with the concept of death as she "disappeared". Plus the seditives, which the scientists said it would cause brain damage. Then, as he laid dormant, far as we know, they never repaired the brain damage.
Of course, the easist solution is giving Tsu a lobotomy as we see in other clone media to control. However, we can't here as we're in a kids' show, despite the envelope being pushed as is. Now the point: remember Tsu's initial reaction when he discovered man created him instead of God -- he rampaged and actively killed the scientists. That is the one scene I carried from that movie, because of the perfunctory carnage (really rare for a kids' cartoon on both shores) and Two, from what is translated and stated, chose to attack the scientists.
Granted, we could blame the brain damage for his overreaction and we should, but the fact the anime never again refers to his reaction to the seditives or Ai-Two could be a tell that we shouldn't, either. It's possible we should simply rationalize him, just as he rationalized his reason for murdering the scientists: the ends justifying the means. Just as he justified the destruction, he justified briefly allying himself with Sakaki, and then justifed removing humanity despite the fact he had a good start with Ai-two.
Then, we really get into nature vs. nurture and that's another topic for another day.
Of course, then, we're treated with his monologues and the opportunity to see where he is coming from (which I'm negative on and I won't go there at the moment) and try to appreciate him like all anti-heroes despite their prior bad acts a la comic books -- Venom, Sabretooth, Mystique, just to name a few.
While Special's take is similiar, but they went a different route substituting Katsuya for Sakaki for the human connection and thus a deeper meaning to the creator/creation relationship. Granted, their Myuutsu didn't have the impact/personality than his anime version did, however, he wasn't as trumped up and had a subtle way to get the message across -- such as a brief glimpse of the canon lab destruction, the detachment to the Rocket-Dan organization, and his obeying Katsuya despite his own issues.
And quite a lot of depth for a game sprite, I know. Collapses.
