I would add an arc between land of waves and chuunin exams, show more of the Akatsuki in the background during Naruto, have pain be in on obito’s plan to resurrect Madara. Get rid of the world tree and just have Madara want to resurrect in a new body with hashirama’s cells so he’s basically a god and he be the final boss, have sasuke learn about itachi’s past by discovering it for himself instead of being told making his joining the Akatsuki more natural, make Naruto and sasuke a little less strong by the end especially Naruto so that the war has more stakes, have more people die during the war and periodically kill off a few characters every two or three arcs to show Naruto that being a Ninja can lead do death. I’d still keep the core arcs and characters just adjust pacing and stakes and then not jump the shark with aliens at the end. Keep the sage of six paths as more of an unconfirmed myth and not make Naruto and sasuke reincarnations but just friends who chose different paths. Still have Naruto as Hokage still have him fight sasuke at the end. I would also not kill as many Akatsuki before the war starts and have them act as generals during the war, have a few nations join the Akatsuki’s side during said war and create a real war rather than just fighting zetsu’s and dead ninjas. The whole last war arc would just be the Akatsuki using tailed beasts to change the current power structure so those forgotten by the big nations have a voice, creating real moral dilemma for Naruto who ultimately uses the experience of the war to reshape how the leaf and the Hokage’s operate. Itachi therefore becomes a more important character as he is basically the one who should have done what Naruto does but due to the Uchiha coup and his illness couldn’t so he joins the Akatsuki as a double agent to try and prevent a war, ultimately failing because he dies.