One problem, just one, and it's one that more of an Easter egg. The original, and I mean the first Naruto one shot ever shown in Jump, was about an actually nine tailed fox spirit with magical powers that went to the human world to find a friend. NOTHING TO DO WITH NINJAS. Want to know why Ninja's are even a part of it, because in the original character design, and in the first episode, Naruto is wearing goggles. The Artist found them to hard to draw so he replaced them with a headband. That's right the entire question of why these Ninjas run around like Demi-gods in colorful outfits is because they were meant to be these spirits that ran around like Demi-god in colorful outfits.
Honestly Naruto would make more sense, and might even be a better concept overall, if you simply accept the fact that they're actually demons and mages. Imagine Fairy Tail if it had an interesting plot loosely based off a myriad of Japaneses, and Chinese mythology. Movie Bob may have his games, he may have his movie but let me tell you, Manga is Weird!
Edit: Oh and as for the story of the actually manga, I'll get into the Anime later trust me, it's surprisingly really good for the first two arcs. The reference the village of mist arc, as one of my favorite Anime arcs ever written. It explains how the whole ninja thing works, it explains each of the characters persona quite well, it provides you with some like-able villains, and then at the ends not only gives you a slightly satisfying ending, but some character development. You find out Sasuke isn't such a stuck up side character as he lets on, you find out Naruto demon's mean business, you also find you that Sakura as about as useful as Rose Tyler.
Like I said the Anime, the anime just does fights better and makes them longer. That's it, at least bleach does something with it's filler from time to time, this just has pointless things that only drag the plot along.