The list of things that are wrong with Naruto goes on and on. One could talk for hours about every Shonen cliche that pops up in the story. One could also ramble on about certain characters (*COUGH*Uchiha Sasuke
*COUGH*) that irritate the hell out of them. But one could also go on about the heartwarming moments, the slow but steady character development, and the pure determination to be his best demonstrated by the title character (who's own list of character flaws could take up a page of their own.)
Then there's the villains. One could argue that they're the best part of the show. They're strong, worthy opponents to the protagonists, who often, before their deaths, show a layer of hidden depth that we haven't seen before. They are serious threats to the characters'lives and safety, but that's not all there is to them, and many people (namely, fangirls) will appreciate this layer of emotional complexity.
In short, there are many things wrong with Naruto. But rest assured that Kishimoto got at least one thing right.