A lot of Pokemon games/merchandise/general stuff I've seen claims that "No Pokemon is evil, only evil trainers make them do evil things". That's kinda dumb considering in Japan, the Dark type is called the EVIL type...
My headcanon is that they're like Mamotos from Zatch Bell. They have their own personalities and tend to work with the humans who suit those personalities, which would help explain PMD Pokemon.
Actually, the japanese word is "aku". I don't speak japanese, but think it's not "evil" with the english meaning. The word is like the Devil Fruits in One Piece (akuma no mi)