I also have a love hate relationship with Naruto.
Tsunade should have been more developed. When Pain landed on the roof the original plan was to have her fight him and get revenge. (I think that would have been some really good story telling) But the author is super sexist and biased towards Naruto and pushed her aside. Also with Tsunade the original plan was to make the Sannin all equal to each other, Tsunade could beat Orochimaru, Orochimaru could beat Jiraya, and Jiraya could beat Tsunade. But then he had to be sexist yet again and make Jiraya and Orochimaru have a bunch of overpowered abilities.
Not only Tsunade but Sakura, and all the other female characters should have been more developed. I seriously hated how he made Sakura grow during the war and presented her as "just as strong" as Naruto and Sasuke she really grew into her own, only to reveal that they're reincarnations of these supernatural Godlike brothers who are the strongest Ninjas.
My biggest gripe with Naruto is that it was inconsistent. When the Manga and Show start we are lead to believe that the Third Hokage was the strongest Hokage and ninja of all time, then as it moves forward we are lead to believe that it was the Fourth Hokage because he sealed the 9 tails into Naruto, then wait no, IT'S THE FIRST HOKAGE. Seriously make up your fucking mind.