Why in the world is this Mewtwo a girl (in theory)? If you have the female with the male that already exists, you can let them mate, kill the parents, and raise the kid as your weapon. Alternatively, for science.
Mewtwo's backstory (and indeed, existence) raises a lot of unanswered questions when one thinks about the details.
Who is the obviously non-Team-Rocket-affiliated group that created it (and was both rich and technologically capable of doing so), and why did they go to the trouble of creating it?
Where and how did they find DNA of Mew - a rarely-seen Mythical Pokémon thought to be (nearly) extinct?
How did they know the exact alterations to make to the DNA to create a Mewtwo physically identical to the original, when no indication is ever given that they already knew about Mewtwo?
How did they come up with the name "Mewtwo", when no indication is ever given that they already knew about Mewtwo?
While the exact nature of the Red Genesect's mind control ability is unknown (Psychic Powers or something technological?), one must wonder what went through Team Plasma's head when they decided to not use a version of it to control their superpowered cyborgs themselves, while also giving/retaining the Red Genesect's ability to control the others and ensure a totally disastrous rebellion.
Unlike in the games, Mega Mewtwo Y seemingly has no drawbacks — it can be activated at will, Mewtwo is able to do it from birth, it bestows enhanced speed without any attributes being weakened, and no mention is made of it being strain-inducing or anything. By all accounts, Mewtwo has no reason to not use it all the time, yet there are several moments where it reverts or otherwise doesn't use it for no apparant reason.
