Basically, Anime and the Movies have always been used to promote the games. So, by showing off the new Mewtwo forme, The Pokemon Company (or whoever is in charge), created more excitement among the facts.
The movie is set in Generation 5, due it being centred around Genesect.
Also, it was never said that Mega-Evolutions existed before Generation 6. It was only in generation 6 that players can unlock Mega-Evolution.
Also, in the Movies/ Anime, legendary Pokemon such as Mewtwo have Uber kinds of power, being capable of doing a whole lot of awesome stuff, presumably why it could Mega-Evolve despite lacking a "strong bond with its trainer".
Alternatively, Mewtwo is so badass, that it doesn't even follow GameFreak's orders.