Pain would've been the main villain in the 4th shinobi world war arc. The Rinnegan would have nothing to do with the Sharingan and Sasuke wouldn't end up with it. Naruto would've continued to learn all his father's jutsus from that scroll that he stole in the first chapter. The Senju clan would have something to explain how they were able to counter the Uchiha clan, besides Hashirama. I would give them either Dead Bone Pulse from the Kaguya clan or Sennin Transformation from Juugo's clan with Hashirama being the only wood user. There's no reason to have two nut job clans that need to be offed in the manga.
Yamato would've been a beast. He would've been lethal like Obito was when he was using mokuton against those Hidden Mist ninjas. The three original doujutsu wouldn't be the only doryoku. Doujutsu besides those would be like any other techniques that Ninja's create. Minato would've had something to explain why he out of all the Hokages had a flee on sight order. What Kishi showed wasn't enough to explain that IMO. Hashirama might have been the most powerful Hokage, but Minato should've been the deadliest Hokage and there are other ways to show that. Minato should've been able to break Orochimaru's control with a contract seal. Minato would've been the one to kill the 3rd Raikage, stopping his rampage by teleporting his head off his shoulders. This would explain why the Fourth Raikage held so much animosity against him.
As other's have pointed out, people wouldn't be changing their minds because somebody whooped their asses and offered to be BFFs. Itachi wouldn't have had a super convenient genjutsu to pull out of his ass to stop and redeem Kabuto. He would've fought to the death leaving his Edo's with free will. Naruto should've had to kill his enemies and his enemies should've gone down swinging till the last drop of blood was spilled, including Sasuke. It would've been Hiashi to sacrifice himself for Neji and Naruto. As his first act as Hokage, Naruto would've fulfilled his promise to Neji and abolished the main family / branch family system. Neji would've been there to see it.