One distinguishing factor: the old Mewtwo's Ability was Pressure, while the new Mewtwo's Ability is Unnerve.The event distribution says it all.
The Mewtwo in this movie is cloned from the Mew from Movie 8.What fans tend to forget is that a second Mew was already introduced into the anime's canon; therefore, it's possible that the new Mewtwo is cloned from it rather than Movie 1's Mew or a generic Mew that merely exists for the backstory.
Anime Team Flare created Mewtwotwo.How anyone officially got the data, we may never know, but Team Flare is said to do what they do for money, and even with what Mewtwo did at the end of the first movie, the fact remains that there was an explosion on New Island. If a guess could be hazarded as to how, they probably hustled it & went there while Giovanni was conspiring with & decieving Mewtwo elsewhere, and may have discovered some sort of DNA leavings either within Mewtwo's tube or where Mewtwo was standing...somehow. Or maybe one of the computers wasn't completely destroyed. The Mew screen may even be extra DNA they found in the strand.
Mewtwo was originally planned to be the original, but the writers changed it to sell more Mewtwo toys to little girls.Notice how the event Mewtwo associated with this movie has Hurricane, a move most likely based on the first movie rather than this one. It's quite likely that the writers, looking to shove as much merchandise as possible, decided that Genesect was enough for little boys and that there weren't enough cute girly Pokémon in the movie to appeal to little girls, so they decided to make Mewtwo into one. And as for why she has nothing to do with the old Mewtwo, it's all part of the same package.
The Mewtwo in the film was created because the original Mewtwo erased Team Rocket's memories.Team Rocket created Mewtwo because they found a sample of Mew. If they had no memory of creating Mewtwo the first time they'd try creating Mewtwo again and since it's their scientists (Dr. Fuji is nowhere to be found since he's dead) making the product their Mewtwo would sound closer to Mew whom Mewtwo is based on. And since this Mewtwo never met any other clones it merely has distrust of Humans instead of outright hatred.
The original Mewtwo will make a return in a future movie as Mega Mewtwo X... In a showdown against this movie's Mega Mewtwo Y. And this is gonna be awesome!
Alternatively, another Mewtwo will appear to showcase Mega Mewtwo XBecause this movie shows that the writers (or the director, more specifically) can say "screw continuity" and expect to get away with it if they feel like it, and as such they would likely rather have a third Mewtwo beause they think it would be better that way. Oh, and don't expect much of an explanation for a third one's origin, either.
Newtwo is the original Mewtwo.Being a being of incomprehensible intelligence and physic power, it can probably change it's mental gender at will.
Douse Drive Genesect was originally Snowdrop.They both have a similar voice and personality. In fact, Douse Drive Genesect has a strange fascination with white lily pad flowers. Could this be Snowdrop trying to remember her previous life?
Mewtwo (in general) is a preevolved form of MewHow else could one explain that two scientist groups using two different procedures in two different environments using two different samplesnote end up with two specimens where the only significant differences are biological sex and the ability to use a Super Mode? The easy way to get such results in game-canon is by breeding. And there is precedent for such: Phione.
Ash remembers what Mewtwo is......because his Aura capability prevented Original!Mewtwo's memory wipe from taking hold.