While Naruto receives a lot of praise, it also attracts a significant amount of criticism. This criticism does not necessarily knock it off its perch, as Naruto is still considered one of the greatest Shonen stories of all time. However, the criticism shows that the story is riddled with huge misses and that the story could have been way better.
While Naruto is praised for how it makes complex themes look simple. The series makes the mistake of oversimplifying its themes, and it does this at its detriment. For example, its themes of genocide are handled like a sneeze; it is shown, but the impact is not as deep as it should be. In contrast, One Piece handles these themes better and does not run over them simply.
The genocide Naruto handles poorly is the Uchiha's. It is weird that the genocide that is tied to one of the main characters only has weight when he is on screen. The rest of the characters in Naruto act like the genocide was akin to a mosquito bite, when it was something that was the result of so much trauma.
Disclaimer: This article reflects the author's views and may contain spoilers.
How Naruto handles the Uchiha genocide poorly

Naruto fumbled its themes of genocide extremely poorly. While it was brilliant that the theme was introduced, as the story is basically one about war, the execution was far from right. The first error was with how other characters reacted to Sasuke's pain.
When Sasuke was in the village, his pain was made to look ordinary. There were not many moments when his teammates stopped to ask him whether he was alright. Kakashi did a good job of teaching Sasuke how to defend himself and to be a shoulder for the Uchiha to lean on, but that was not enough. This is why Sasuke's leaving the Leaf for Orochimaru comes as no surprise.
It can be somewhat explained that the Konoha shinobi were kids, and due to that, they could not understand Sasuke clearly, but their older years are still punctuated by that aloofness. There is no regard for the Uchiha clan, the source of Sasuke's pain. It seems like there is no effort from the supposed close friends of Sasuke to try and uncover Itachi's reason for the genocide.

Eventually, the Konoha ninja find out that their village was responsible for the Uchiha's death. Do they react? They barely do; the nuance that the protagonist approaches things with ceases when he meets Sasuke.
Sakura also does not help things as she tries to harm Sasuke, the person she claimed to love. Nobody in the series seems to be torn from the fact that the Konoha leadership eliminated an entire clan; there is no cognitive dissonance.
Final thoughts
The truth of the Uchiha massacre deserved more screentime. Viewers needed to see how the various citizens of the Leaf reacted to the state-sanctioned murder of an entire clan. It should have also spurred on some sort of overhaul or action against Konoha's leadership system. None of that is seen in the series; instead, it is business as usual.
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