I'd change so, so many things starting after the Pain arc.
I'd make Danzō live longer and become Hokage in order to make a "Konoha Lockdown" arc (not my original idea).
I'd make Madara a less important character, as in his only purpose would be to tell the audience that Tobi isn't Madara. He'd still do his moves and whatnot but once Kabuto is defeated, Madara is gone.
I'd make Infinite Tsukuyomi a decades long Uchiha conspiracy with multiple past Uchiha in on it. No Kaguya.
I'd make Obito or Orochimaru the final villain.
OH. And no Rin bullshit.
I'd also add in a new villain between Part 1 and 2 that can actually pull off a revolution (looking at you, Sasuke). He'd ask ninjas to rise up against the warmongering Daimyō and their Kage dogs. He'd begin the revolution by attacking Konoha to bring about imbalance in the Shinobi World, leading to better opportunities for the revolution. Of course he'd fail in the end, though. The K11 would get more development here as well since there's be little to no Naruto or Sasuke in the arc.