i think it's the fact that naruto in it's core never changes, most of the characters have zero development (especially characterwise) and the basic story of the everlasting konoha kinda annoys me.
apart from that there are from time to time storytwists that are just insanely retarded. like the whole way sasuke's character develops. like the way pain changed. like the mass-rezz-no-jutsu of pain. like when sasuke decided to attack the kage-summit. ...
the worst thing about naruto is naruto itself.
that was the worst thing in naruto normal, but momentarily i like his character-development. i mean sadly he becomes kinda boring, but at least he's not completely retarded anymore.