The possibility of "evil" in Pokemon has always been something that's intrigued me, but the execution has always been the troubling bit.
Pokemon Colosseum and Gale of Darkness played with the idea of shutting down a Pokemon's heart, but that's not necessarily "Evil" on the Pokemon's part. My reasoning is that the Pokemon, having its heart locked, acts out of aggression and primal instinct, not evil intent or malicious purpose.
In the anime and manga, we've seen examples of Pokemon that are considered "bad" based on the actions and commands of their Trainers. However, we've never seen a Pokemon that has been truly malicious for the sake of being evil.
So, no, I don't think we'll be seeing any sort of "Evil" unless it is somehow influenced by humans or a third-party force. Pokemon have always been portrayed as creatures that enjoy battle and can, in time, learn to enjoy the company of humans and battling for them as partners.
In every example of "Evil" in Pokemon, the cause has always been humans or a third-party: Mewtwo was deemed "evil" because he thought that TR's actions in creating him were selfish and evil; the Pokemon belonging to members of evil organizations are only considered "evil" because they follow the orders of their Trainers who, as shocking as it may seem, are human also and more than likely have compassion for their Pokemon that they mask behind malicious intent in front of the public; Even supposedly "Evil" wild Pokemon in the anime have been revealed to only be "evil" because of mistreatment by a former trainer or by fellow wild Pokemon.
"Evil" just isn't in Pokemon.