I agree with the points here, but, just allow me to play devil's advocate - aren't certain pokemon way more intelligent than the animals in real life? Wouldn't they be able to find an incentive to be 'evil' all on their own? It has happened before - if you watch a certain episode of pokemon, you'll see that a Togepi is indeed 'evil'. Or has a lack of good if you wanna be philosophical. And no, it had no trainer. It was actually, physically, "bad" on its own.
Would X&Y have pokemon that have hidden motifs such as that? I mean, in the games, independent ideology is indeed possible with legendary pokemon.