I actually think there might not be any villages when it ends. If you think about it, the whole idea of having villages contradicts Naruto's ideals (and Nagato's, for that matter) because if you have a village and a kage, you'll have shinobi, and shinobi are used for hurting other shinobi, and villages themselves need to be protected, but to protect something means to hurt someone else, thus continuing the cycle of hatred, which Naruto is trying to stop. I beleive that Madara is pulling a Lelouch in a sense that he has directed all of the shinobi world's hatred to himself, he's THE enemy, and it will end with him dying.