Subject: About Mewtwo...
Author:
Posted on: 2015-05-01 23:50:00 UTC
You're right about not being able to use that specific Mewtwo (then again, he did fly off into the night after Mewtwo Returns, never to be seen again...), but, from a PPC perspective, Mewtwo is hardly unique. As EvilAI mentioned, the latest games basically state that each game (if not save file) is its own parallel universe, so there are potentially millions of Mewtwo out there.
Meanwhile, according to the journals in Pokémon Mansion, Mewtwo isn't an artificial clone of Mew; Mew gave birth to it. No human intervention was involved. The Pokédex contradicts this, of course, but the Pokédex routinely contradicts the laws of physics, so I tend not to pay much attention to it. (Also, "years of horrific gene splicing and DNA engineering experiments"? Mew was discovered in July, and Mewtwo was born in February. Yeah, that's "years"...)
My personal theory is that, in times of stress, Mew can recombine its own genes to produce a Mewtwo child. It makes sense, since Mew isn't exactly a big fighter. Of course, that's just headcanon, but it explains the Mewtwo in Pokémon Ranger 3 and Pokémon Conquest better than there being only one Mewtwo.
I guess it all boils down to which parts of canon you choose to believe. I don't know whether headcanon is acceptable in Agent backgrounds, but that's how I'd get around the problem. And if that doesn't satisfy you, again, there's plenty of canon that can be used to achieve the same end.
Then again, maybe this is all moot, because the original topic was finding a Pokémon that would attack humans, and any alternative Mewtwo wouldn't necessarily share the animé!Mewtwo's misanthropy.