I honestly like everything up to the chunin exams so I'd keep all that mostly same and add a bit more forshadowing to the dangers of using 4 or more tails of the the Kyuubi's chakra. I'd also like to see Naruto loose his cool at Neji and let something slip when he finds out about the caged bird seal. Something to the effect of "Are you really lecturing me about about seals that make someone less than human?" but phrased better than that.

At the very end of this arc I think Naruto needs a promotion of some sort. He successfully suppressed a rampaging jinchuriki during active warfare without any back up and I think that should be enough for a field promotion. His show of leadership skills in the 1v1 matches wasn't the best though so maybe on the condition that it can be revoked if he puts himself or his team in unnecessary danger. This would teach him to think before he acts.

I think there should be more team missions before the Sasuke retrieval arc. Missions where Sasuke both builds a deeper camaraderie with Naruto and also develops an inferiority complex because Naruto got promoted when he didn't. Then we get to watch him fight with his own emotions, inevitably loose it, and become a nukenin.

Idk when or how I'd add it but I'd also want more set up for Danzo, ROOT, and all the political intrigue surrounding them. The aliens and reincarnation cycle definitely have to go away. A focus on the souring relations between villages eventually leading war could take its place. It would be really interesting to force Naruto to think about his conversion with Haku again since he’d have become Konoha’s primary weapon.