Naruto as the villain
A friend and I were discussing Naruto recently, and he proposed that Naruto and Konoha are the real villains in the series. More or less the 1st Hokage was an unelected dictator that ruled by strength and imposed his ideals on the society he lived in, creating a social model that forced the world into peace through control. Rendering the bijuu as weapons, he essentially turned the shinobi into slaves of their respective villages as a form of oppressive moralism. Where the weak are coddled and fostered like a virus, people are forced to allocate their resources to protecting people that have no right to exist.
Madara saw the inherent moral problem in this and tried to overthrow Hashirama as to establish a world where there are only winners, where everyone has freedom and the losers die off. Hashirama's and the Third Hokage's actions lead to countless conflicts and the creation of horrible villains like Orochimaru, who would have been killed early on in a Madara regime. So Madara recruited Obito, an Uchiha who had seen first hand the intrinsically unfair nature of the world. Because Obito had to get crushed to protect a weak little insect (Kakashi is and always has been far weaker than Obito, relying on cheap borrowed power, despite fanboy rage to the contrary)
So this basically leaves Naruto as the unwitting villain, protecting a corrupt and oppressive village that only brings conflict and disgrace to the world. Supreme ignorant in his moral beliefs, Naruto fails to understand himself or even the greater consequences of his actions. Clinging to childish, idiotic beliefs such as "Never give up" and conditionless friendship, Naruto embodies the naive and self-destructive idealism that comes with morality.
While I don't agree with him, I thought it was an interesting take on Naruto. We sort of take it for granted he's the "good guy", but really Obito is trying to create world peace in his own way and Naruto could have just resigned himself to death against Pain and nobody in the village would have been hurt or killed to begin with. In a large sense, it's his father's fault that the village was targeted by Akatsuki. Had he just sealed the 9 tails in himself and died, itd have all been over.