What else can you expect? Also the anime was been very inconsistant, which has led to the theory that the anime is completely different from the game.
As for the fundamental laws of Pokemon, a certain Pikachu once KO'd a Rhyhorn (Ground type) with Thunderbolt. That same Pikachu's Thunderbolt failed to destroy a certain Swanna because it was hiding behind an Aqua Ring. Aura Sphere has set a record for having missed.
The most logical expectation might be that Mewtwo is almost a completely humanoid Pokemon, so it doesn't need a trainer to actually set itself into a mega form. Also since it is artificial, maybe a few tweaks or something happened, that made it capable of Mega Evolving itself.
Hope I helped!