Did you know that while the dubbed American (4Kids Entertainment) version of this film portrays Mewtwo as an inherently evil, bent on world domination psycho (and ends with the message: fighting is bad, kids), that the original Japanese script in fact depicted a far more tragic Mewtwo, one who had been betrayed and used by humans, and felt without purpose or meaning in a world where he was neither person nor pokemon. He never meant to destroy the world, he only planned to prove he too had worth, and in general, that existence has worth. In the end, he realised the nature of his birth was irrelevant, worth comes from within and life is what you make it.
Also, Mew was a **** who basically said clones are inferior, and will always lose. He essentially instigated the fight at the end of the film, in the Japanese version.
There's also a fantastic double entrendre at the end, where the trio of heroes says, 'Why are we here?' 'I don't know, but we're here, so let's stay awhile'. They're referring of course to their physical location, but accidentally stumble upon the answer to Mewtwo's dilemma - it doesn't matter why we're here, all we know is that we're here, so let's make the most of it.