You mean like in Chrono Cross?
My answer would have to be some I wouldn't expect anyone else to come up with before I announce it, and then have everyone go, "hey..."
I would like the story of an RPG to be told from the point of view of the villain. Something like a guy trying to take over the world. But he's not evil. He's just misunderstood. People don't understand that he's trying to take over the world for the good of the world. Kind of like if someone were planning a coup d'etat in the United States of America under the Bush administration. Such a thing would be admirable, but highly misunderstood and surely the person leading said coup would be considered a villain. So, you follow the villain in his attempt to take over/improve the world while the "good" armies and whatnot attempt to stop him. Actually, I've been thinking of writing said RPG for some time.
I'm surpised such an RPG has never been made. Correct me if it has.