We know that there was a move called Psystrike that was introduced in Generation V that is exclusive to Mewtwo and Kusaka would probably want to showcase that. Thus, Mewtwo will probably appear in either BW or B2W2, most likely the latter since the former is almost done and Mewtwo wouldn't really have a role in the chapter. But when Mewtwo eventually does appear, what role do you guys think he will serve?
To get this thread started, I'll post my own theory. Genesect is a Pokemon with similar origins as Mewtwo, with Mewtwo being Rocket's scientific creation and Genesect being Plasma's scientific creation. Since they are practically parallels, they will probably battle which gives Mewtwo the opportunity to show off its signature move. Oh, and because of the PWT it will get to meet Red and Blue and finally realize that they are no longer petrified. And to top it off, Kusaka tends to borrow elements from the anime at times (i.g. Mewtwo's armor) and the next movie is going to showcase a battle between Mewtwo and Genesect so yeah).
Okay and a reason for Mewtwo to go to Unova is because it lost Sird in the chase and it went to Unova because it thought Sird was there for whatever reason. (Maybe because it found out about the PWT and thought that due to a large gathering, she would go there to seize the Pokedexes?) And then when it explains what it was doing for the past 9 years (time between Emerald and HGSS was 3 years, time between HGSS and DPPt was 1 year, time between DPPt and BW was 3 years and time between BW and B2W2 was 2 years so 3+1+3+2=9 years) we will get to see yet another Sird cameo. Oh well, at least Mewtwo can rest after its battle with Genesect.