It's already filled with inconsistency, plot holes and overall stupidity so why are you expecting logic? I mean right off the bat they aren't even really ninjas, they scream their battlecry and their moves out loud. The exact opposite of a ninja.
How others see Naruto
Ninjas = Awesome
Flashy Powers = Awesome
Eye Powers = Awesome
Combine them all and their bound to be awesome, amirite? Well not in Naruto's case. And ignorant main characters? I find it somewhat ironic that most of the main characters in hyped media think their doing right but actually are failing to see the big picture. Ex; Death Note, Code Geass, Bleach, Attack on Titan, FMA etc. Honestly we can just reference Akumetsu ending as the solution to all of this.
Though I get the idea that the system is full of idiots. The good guys train and develop skills and start fights with other villages basically making every single 'villain' in Naruto. The bad guys are all fucked up because the good guys went and sent shinobi and killed their parents, loved ones etc or did something with the tailed beasts. Personally I found myself rooting for the antagonists for the majority of Naruto and especially Obito even though his reasons were laughably stupid.
The plan that Madara came up with is actually pretty legit because
And even though Madara would have complete control over the world he stated he wanted justice for all, no more wars and everyone to be reunited. Sorta like the NGE plan but without everyone united into one person. In my opinion even if Naruto becomes hokage and lives a long life united all the villages war will eventually break out.