In the first movie, Mewtwo erased everyone's memories of the whole ordeal after witnessing the bonds between humans and pokemon revive the petrified Ash.
Ash later reunited with the same Mewtwo who had gone into hiding in the Johto region with the clones from the first movie, though his memories of their first encounter never recovered, thus limiting his knowledge of Mewtwo and its capabilities.
It sounds like the Mewtwo in this new movie featuring Genesect is a different one (no idea how it came about, though there's a special episode in the works to explain just that), so that's the best explanation I can offer. --- Playing) Fire Emblem: Awakening, Guild Wars 2 Waiting) Pokemon XY
did he really forget or was that more bad transaltion? --- 3DS FC: 4940-5445-8767 It is a remake, not my fault you people think ports are remakes (but only on Nintendo systems)-Demondog666 on Kid Icarus Uprising