Zone of the Enders 2 also did a fantastic job with cell shading (though as I normally abhor the style I'm not sure if my opinion counts as much here).
As for anime in general...hard to say. I'm distinctly a fan of anime, in most of its forms, and have been since I was very young. I tend to think what drives people away from it is said people noticing all the flaws all at once, rather than over time like the (sane) fans.
Flaws being repetitive characterization, character design, and some truly banal (and repetitive) scripting. These things do tend to crop up, and Naruto unfortunately features two of them as primary traits for its main character ("I never give up!" "I have limitless supernatural power!" and "I have lines indicating all this!" specifically). Speaking from an actor's perspective, the english dub of Naruto also suffers from VA's who are accurate to their characters but find aspects of the script a bit awkward, or who seem a tad amateurish (And I have no idea what threw Freeman off on Itachi).
That said, some anime is absolutely phenomenal, for story: Cowboy Bebop and Full Metal Alchemist (with its hastily-invented second half, no less), Wolf's Rain (even with the type of "look how artsy we are" bullshit ending that Evangelion pulled and expected not to be laughed at for), etc. The trick is finding the good anime (no s for the plural. "You wouldn't say Chineses." )amidst the loads of not-so-good stuff. It's like any other medium that way: it even has its own version of the incredibly stupid "indie music elitist" type fans.
In case it wasn't obvious from the rest of the post, I'm a fan of Naruto. Or at least I maintain enough interest in it that I can apply the title to myself. This comes out of my liking it for it's good points (relatively original approach to fighting anime genre in places, the generic appeal of fighting anime shows), while being able to recognize and even laugh heartily about the bad (Kishimoto is an INCREDIBLY inconsistent writer).
I find this makes me a happier person than the people I keep running into who will seize and harp on any bad aspect of a show/movie/series/etc. they can find or, barring actual flaws, invent. Probably a better one too, but I'll ignore the temptation of the high horse and not state that as a definite.
So two final notes!
One: Damn you people and your positive reviews of Ninja Storm, now I'm vaguely interested in it. I mean, what does it say when almost all the comments on a game are positive, when almost all the people commenting hate the source material?
Two: He wears orange because it's an utterly stupid color for a ninja to wear. This is one of the examples of Kishimoto's writing being GOOD: there are repeated comments by other characters in the manga/show that the outfit is ridiculous (Literally, "What kind of ninja wears orange?"). He made him terrible at being a ninja AND annoying as a character at the start, presumably to allow for character growth. Exactly how much of that growth has been ACHIEVED is a subject for debate in a forum where there's more than one fan posting.
....dear sweet hamster jesus, I have to stop writing such long posts.