Naruto not being an underdog isn't a problem at the end of the day everything comes down to execution but what causes issues for the series is the contradictory elements of Naruto story. Mainly while Naruto is not an underdog the story frames him as one and that causes thematic conflict. And it's why until now with have constant arguments about whether or not Naruto was an underdog, when you convey contradictory things your audience will have contradictory interpretations.
Firstly, let's explain why Naruto isn't a underdog even in part 1.
- He has the Nine Tails which gives him lots of chakra and protects him in battle
- He is a Uzumaki which also gives him a lots of charka
- His was able to learn high level techniques in days or weeks like the shadow clone jutsu or resengan
- His able to get training from powerful teachers like Jiraiya due to connections
- He was destined to gain the power that could save or destroy the world
So how does the story treat Naruto like an underdog. Well many characters in the story treat him like his untalented and useless and won't achieve anything:
- Even in Part 2 Naruto is compared to the six sage son who was not talented and had to relay on others for help
- The bridge builder: A Hokage is powerful and wise, you are puny and weak.
- Lee in the Chunin exams states that Naruto is a underdog like him saying that it would be a good thing if he beat Neji proven that failures can beat genius
- In the Neji match Naruto is called a failure
- After beating ninja Naruto says that his clone justu was his worst implying that he improved it with practice not because he was also a genius
- Tsunade calls out Jiraiya for putting false hope in Naruto that he could be a powerful ninja or master resangan
- Orochimura: Trust me, I've always had a good eye for talent with that one all I see is insipid mediocrity
- Everyone who called him and useless and stated that he didn't have talent
- He was constantly contrasted against geniuses like Neji and Sasuke
Now people like to say that Naruto was an underdog because he was an outcast. However being an outcast is not the same thing as being an underdog. An outcast is someone who is rejected because of who they are, while an underdog is someone who is innately less talented and a lower chance of winning compared to his more talented competitors, they may be some overlap but their not the same thing. Say there's an guy who because his ugly is rejected by everybody thus his an outcast however his able to master instruments in days because of his talent is he a underdog? No, because despite his suffering his still talented and has an innate advantage compared to his competitors that doesn't mean he didn't suffer but his an outcast not an underdog.
If you want another example look at Gaara, he was treated poorly by his village but his not treated as an underdog. Why? Because that doesn't change the fact that his very talented due to his sand ability. Furthermore, just because the nine tails made Naruto life hell doesn't change the fact that it gave him a mass amount of charka, something can be a disadvantaged but at the same time be a privileged.
Also Kishimato did a very POOR job of portraying Naruto as a social underdog. We are TOLD that Naruto was mistreated in the past but we are never really shown it in the manga itself. The hatred he gets is only present in the beginning of the story and then slowly goes away. We never really get to see the villagers mistreating Naruto once he becomes a gennin. Where is the random villager / waiter who spits in Naruto's ramen? There's a reason why people viewed Naruto in part one as a underdog and not an outcast and
that's because that's the thing Kishimato put emphasis on.
But people didn't know about the nine tails or his Uzumaki linage
That makes it worse. Why is Kishimato constantly having characters treat Naruto as if his a useless failure when it pretty clear that the nine tails gives him lots of potential and it's clear his not a underdog when his able to master high level justus at a young age? It's redundant. Plus, the moment Naruto saved the village during the sand attack or mastered the shadow clone justu he should have not been treated like an underdog anymore.
But Naruto couldn't control his charka due to the nine tails
That makes Naruto a late bloomer not an underdog. He had potential but he was limited but when he got the required help then he became powerful, it's just that compared to Sasuke and Gaarra his potential just didn't show immediately.
But Naruto worked hard
I'm not trying to downplay how hard Naruto worked he definitely did train an lot but so did Sasuke and Neji, plus Naruto had innate advantages when it came to getting stronger thus he didn't get as strong as he is with hard work alone. If any other ninja had worked just as hard or even harder than Naruto they wouldn't be as strong as he was because they don't have his gifts (e.g. Rock Lee)
Hard Work vs Talent wasn't that big of a theme in Naruto
- That doesn't excuse the fact that it was poorly written it was handled awfully even if it was a small theme.
- All the themes in your story should work together if you have a theme that gets contradicted by other themes you shouldn't included it in your story.
- Hard Work vs Talent is a theme that's going to resonate with viewers more than abstract concepts like 'The Cycle of Hatred' since Hard Work vs Talent is personal and more relatable.
Also Naruto being an underdog is backed up by the author, so people weren't making it up:
Masashi Kishimoto: My childhood wasn't all that happy. It may have sounded like it was all good in my journal entries in the manga volumes, but that was in order to make it interesting for the readers. Like any person, I've had hardships in my life. I was not the centre of anyone's attention in school, rather sitting on the outskirts. I didn't do well in everything. I didn't excel in studies nor sports. So
I can understand Naruto's feelings of being an underdog. I don't really like people who are too perfect. [laughs]
Thus, the issue comes from the fact that Naruto tells us one thing but shows us another.