Differences and exclusives...haha.
Yeah, whatever helps you sleep at night. They just knew damn well a ton of morons would buy both for what is basically the exact same game. It would have made much more sense just to merge the two, since they're basically identical.
But hell, they sell more this way.
I bet Gen6 is going to have 3 pokemon games and possibly 6 in the sequel to them. Y'know, split each version into two and change one pokemon, sell it for full retail. Once they bankrupt their fanbase selling them 37 copies of the same game with a different title, maybe pokemon will finally stop its rampage.