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.
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.