1) Didn't continue developing several of the K11 and other characters including Sakura, Neji, Hinata and the hyuugas, Ten Ten, Sai, Baki, Genma, Kankuro, Temari, Kiba, Shino, Kurenai, Yamato, Taka, etc.
2) Skipped or shortened several edo character developments including seven swordsmen of the mist, Hanzo, Sasori, Deidara, Kakuzu, Kimimaro, Sakumo, the Sound Shinobi, Chiyo, Mu, etc.
3) Left out Hidan's backstory and shortened his combatability and fights due to editors and publishers walking all over him.
4) Didn't give Naruto an extra element or legendary weapon like Sasuke.
5) Didn't give Sakura a backstory, clan or special technique beyond medical jutsu, even though he foreshadowed he would.
6) Kept Gai alive.
7) Didn't bring Edo Hiruzen back in his prime
8) Didn't give Akatsuki subordinates or rogue squads for the k 11 to fight
9) Killed off Orochimaru and didn't make an extra faction for characters to fight and thus develop.
10) Cut most of the Jinchurikis from the story
11) Didn't develop hidden rock much
12) Kept Sasuke away from team 7 for too long in part 2 after their first reunion
13) Didn't let the Kunoichis fight Konan in Pein arc