As for the prophecy, it's probably easier just to say that it was wrong, that either there was never a "Chosen One", or that the role of the Chosen One was not that of a messiah, but simply to set into motion the events that would lead to the destruction of the Sith at Endor. And as far as we know, the Sith were destroyed: giganto-Gollum and a kid in Vader cosplay do not an ancient and terrible order make. And maybe that's what Luke means when he says we're done with the Jedi, that the Jedi were justified by the continuing existence of their mirror image in the Sith, and that while the light and dark side of the force persist, the rules of the game have changed.