Naruto lost, because Sasuke is not saying he will work with the alliance. He has no answer to Pain's question and no way of assuring the world will remain united or peaceful. In the end yeah he's just one dude, and a kid at that. He got Sasuke to admit they are friends, and to fight to a draw. But even Sasuke says he may oppose Naruto again one day, and he won't acknowledge the rest of the alliance. Sasuke doesn't have any intention of working with the Go-kage or the TB.
Also, I think Naruto has a bigger issue in dealing with the other villages. I doubt they are going to be too pleased to give Konoha all 9 TB and the Rinnegan.
Sasuke lost because he couldn't kill Naruto or accomplish his revolution alone. They both lost an arm, and they realize they're connected by blood and need each other, whether they want to need each other or not. That's what brotherhood is.
Kishimoto is telling us that mankind has no future, except to either learn to live together under common needs, or to die together in the peace of the common grave.