Of course Nagato was right and Obito+Madara are right too (if that really is Madara´s intention).
Their way isnt evil, its the only way. How are you going to judge something if there isnt any alternative to it?
The "good" guys are a bunch of pathetic hypocrites, talking about peace but never doing something for it. They are just hoping that someday peace will find them, something that will never happen. They dont deserve peace if they are not willing to do anything for it.
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Even Obito who is alot younger realized that, thats what he meant when he said that the concept of hope is just giving up (..and waiting for something thats never gonna happen).
But Im sure that Kishi will deliver a flowerpower happy end in which a teenage-foxboy creates some crap like "true peace". He would need to change the emotions and thoughts of several billion people but who cares, he´s the maincharacter he can do anything..