Re: Pokemon X and Y: Villain Speculation?
Here's an idea.
Maybe it's not a team, this time.
Maybe it's the Legendary Pokemon themselves. X could seek to protect life (both males and females have at least one X chromosome) while Y tries to destroy at least half of it (only guys have a Y chromosome).
It could also go with the idea of genetic abnormalities. Perhaps they come to view humans as that...?