Interesting......
I would have liked to change a few keypoints in Naruto actually.
1) Naruto and the 9 tailed fox never become "friends" or allies and we would see more of the nine tail possessing Naruto like he did in the Pain invasion arc. It would have kept things more interesting and would have progressed the plot more...... For example Naruto would start to lose control more and more even when nothing is happening. Soon he would leave the village thinking to protect everyone and the order is given to go after Naruto. At somepoint in time Naruto comes in contact with sasuke and after a brief fight sasuke would realize that Naruto is losing the plot thus he tries to help in capturing him ( read the second point to understand sasuke)
2) sasuke doesn't join akutsuki (sorry for spelling) and becomes an anti hero, he basically goes after the akutsuki members with his own group to try and save the tailed beasts/world. Since he is an anti hero many villages (including konoha) would not like him and be somewhat warry of him...... However after sasuke confronts Naruto konoha would use sasuke or rather hire sasuke to help.
3) this one is separate from 1 and 2.......in short Madara and hashirama are evil and they have planned everything from the start. (Things would go down the same way they did, however once hashirama meets madara on the battle field he would turn against the ninja alliance). Madara and hashirama are both looking to become immortal beings (in other words god) so they fight the ninja alliance and the 2nd, 3rd and 4th hokage.