Thought about this last night. Cinnabar has that destroyed lab with Mew documents. Inside, there are scientists that use very Rocket-like Pokemon. It's similar to the movie where Mewtwo destroys the Rocket's lab and escapes to some off-coast rickety ol' island-like cave thing to clone its own Pokemon (Cerulean Cave?)
I'm just thinking that since the Mewtwo story wasn't really a "big thing" in R/B/Y (it was a small post-game side-quest with brief explanation, if you chose to read them, on Cinnabar Island), the company may have tried to better explain what occurred through the movies. Makes sense, anyway. Also, someone mentioned maybe they took over Silph Co. for the MasterBall... After Mewtwo's escape, is it not possible that they wanted the MasterBall to firmly capture and seal Mewtwo from ever disappearing again? Especially since in-game, Giovanni is automatically Badge Eight, meaning any caught Pokemon *has* to obey. If he used the MasterBall on his escaped-Mewtwo, it would have to obey him and conquering the world would never be easier for him.
Gen VI ought to be a way for them to actually explain, sans movie references, what happened with Mewtwo, and if Team Rocket was ever involved as shown in the film (and minorly suggested in the games).
Again,
- Giovanni employs Rocket scientists to make the world's most powerful Pokemon from Mew's genes /non-canon
- Scientific Lab on Cinnabar (with scientists carrying "traditional" Rocket Pokemon) is destroyed /canon&non-canon
- Mewtwo escapes and isolates himself on an island /canon&non-canon
- Silph Co. is taken over by Team Rocket and Giovanni. Silph Co. is famous for its PokeBall technology; thus, Giovanni was probably after a MasterBall /canon&speculation
- Giovanni plotted to use the MasterBall against Mewtwo, his escaped "creation" /speculation
And it's possible the new team (or maybe TR returns) finds the scattered papers at Cinnabar Lab and Mewbuu is the result of that? We shall see.