How many episodes it takes to finish a fight. (It's like that joke: how many saiyans does it take to change a light bulb? One but it takes 12 episodes.)
The filler episodes.
The same old one liners that come up over and over again.
I don't particularly like how the show seems to mostly be about Naruto. Granted the show is named after him. But with so much focus predominantly on one character, it gets kinda difficult to see the character development of a lot of the other characters.
Lack of variety during his fights. The multi shadow clone jutsu I understand. Rasengan a little. But anytime you can predict what persons actions will be for any three fights in an episode you haven't seen before, and be right, something's wrong.