On the topic of whether Pokemon can be good or evil, I don't think it's any different from them, than it is for humans. I think any Pokemon can be good or evil, if that is what they choose to be, however I agree that they can also be manipulated into doing evil by their trainers, even if it isn't what they want to do. Pokemon are obviously far above the intelligence of most real life animals, so decisions like these are something they're capable of making, however there doesn't seem to be much emphasis on these sides of the Pokemon, since most Pokemon we see in the anime are owned by trainers, and usually stay loyal to their trainers after capture, while this kind of thought usually isn't given to wild Pokemon. It's mostly with legendary Pokemon where this is brought up (like this discussion xp), however with those, being evil is mostly caused by something that has happened to them, and not necessarily by choice, like with Mewtwo. If Giovanni hadn't claimed to be above Mewtwo in any way, I doubt he'd have turned out like it did. Of course it's still possible, as it was also lead with him knowing that he wasn't even a real Pokemon, but I think he felt like he was, when Giovanni claimed to be his partner.
One thing though, I think Dark type is known as evil type in Japan, so whether Pokemon can be evil or not may already have been decided back in gen 2.
But yeah, can't say much for the whole good/evil relation between Xerneas and Yveltal, however I'm not turning the possibility down. Though the concept is pretty cliché, it works :p