Naruto's success comes as no real surprise; the manga found many fans with its interesting characters, complex (but initially well presented) themes and a cliche but overall decent storyline, with many viewers and readers alike using it as their gateway to the greater world of anime and manga. This certainly doesn't come as a shock, since there's something in Naruto for readers from all ages; the cool techniques to captivate the kids and teenagers, the various aspects and popular elements mixed together in the manga, from romance to the cold war struggle throughout the manga between the villages to the morally ambiguous villains as well as discussing what brings people to hating one another for so long.

The manga's popularity isn't exactly a secret or something that's difficult to understand. What is difficult for many to understand, however, is the religious like following it has gained from fans around. I'm not talking about popularity here, I'm talking how whenever you find a Naruto fan, they legitimately tell you about how the manga is so perfect and how the anime ruined the manga, seemingly unaware of the manga's flaws or problems.

The problems start with the story; it's nothing we haven't particularly seen before (person wanting to become a leader), only here we have the themes of wanted to be accepted and acknowledged by society and fight discrimination both on a local and eventually on a more worldwide scale, which is pretty epic in scale once you think about it.

The themes aren't bad in themselves, but they dominate the manga and make the characters so defined by those themes that all their other, more interesting personality traits are completely shoved into the background or ignored. This is particularly shown in how the show sets up rivals to Naruto who always have some kind of contrast to Team 7, which gets incredibly repetitive and overblown after a while and takes away from whatever merits the story has.

This is problematic the closer the manga edges to its conclusion, since it then becomes clear that the writer had no idea what to do with the themes present in the story and ends up contradicting each and every single one of them. What we're instead left with is a broken mess narratively speaking, since the manga up until the early post-timeskip arcs feels nothing like how it becomes later on.

The power-levels are also broken to hell and back, since the show is willing to contradict its own logic and add aspects or themes that simply didn't exist earlier on in the show. This is especially grating near the end of the manga, where many plot elements that were unique and only slightly relevant completely take control of the show (the Sharingan being an excellent example of this).

Character dynamics largely revolve around Naruto, who admittedly is a well-developed and increasingly more mature character the longer the manga progresses. The problem is that literally every character in the show is some kind of contrast to him, and they're so defined by him that later on in the manga, you have a better chance of seeing a character mentioning Naruto than you do of them mentioning themselves. Everyone compares themselves to Naruto, even earlier on in the manga. This becomes incredibly problematic when the themes start contradicting themselves later on in the manga, since so many of the characters are defined by the themes yet none of them ever point out Naruto's hypocrisy in believing in what he did at that point.

Speaking of Naruto's cast, this brings us to yet another problem that plagues almost aspect of this manga; balance.
Naruto is easily one of the most unbalanced manga series I've ever read (especially as far as characters are concerned), with certain characters receiving a ridiculous amount of attention (Shikamaru and Kakashi stand out as particularly well-developed characters until the final arc) while others receive next to no attention outside of the arcs where they're introduced or focused on.

Others are clearly only present as a contrast of Naruto or Team 7, leaving us with them suffering as well when Naruto changes focus and contradicts himself; nobody points out the contradictions, everyone keeps hailing him as a savior, and the dynamics are completely ruined.

The artwork is generally pleasant but also has a nasty habit of ink being sprawled all over the place when their are action scenes, making it hard to follow up (especially near the end of the manga, probably due to the artist being tired or drawing so many continuous action scenes again and again).

The character designs have clear distinctions and identities of their own, which is a massive positive and makes it easier to remember the manga's enormous cast of characters.

Naruto is a manga that ultimately is carried simply by nostalgia alone and becomes increasingly inconsistent as it progresses.
This isn't a bad thing, but the flaws become larger and more difficult to swallow the longer it lasts, leaving a bad taste in most readers' who have read the manga to the end.

It has some exceptional qualities, but those are hampered by the contradictory development that takes place later in the manga, meaning that an otherwise decent manga slides into being below average and increasingly forgettable.

In other words, it's a complete disappointment that leaves a bad taste in the average reader's mouth and is ultimately a product of a bygone era of anime and manga that simply didn't stand the test of time as far as quality is concerned.