The best the story can do and still make sense is having his goal require both unearned advantages and training
But what the story actually does is having all of his greatest powers granted by others, completely unrelated to any of his training. In the early to mid story, he only survives due to fast healing and occasional berserk-god mode granted by Kurama. In the late story, he gets powers from all nine tailed beasts and the ghost of his ancestor. None of these require or rely on any training; they would work the same on anyone.
What tricks are there that he learns for himself? Shadow clones, which he miraculously learns in a few hours where others struggle for years and almost always fail - because it's suddenly really emotionally important to him, not because he trained really hard at anything. Rasengan, which he improves beyond the original, uses a clever hack and not training, and is the only thing that's really his own.
In the early to mid story, he only survives due to fast healing and occasional berserk-god mode granted by Kurama.
"If it wasn't for X he would have died" is not the same thing as "only survives due to X". X could be one of a set of things, all of which are necessary to his survival. Both these unearned powers, and training, let him survive; without either one he would have been in trouble.
What tricks are there that he learns for himself?
"Learns a trick" is not the same thing as "training". He can learn to d...
As people who care about rationality and winning, it's pretty important to care about training. Repeated practice is how humans acquire skills, and skills are what we use for winning.
Unfortunately, it's sometimes hard to get System 1 fully on board with the fact that repeated, difficult, sometimes tedious practice is how we become awesome. I find fiction to be one of the most useful ways of communicating things like this to my S1. It would be great to have a repository of fiction that shows characters practicing skills, mastering them, and becoming awesome, to help this really sink in.
However, in fiction the following tropes are a lot more common:
Example of exactly the wrong thing:
The Hunger Games - Katniss is explicitly up against the Pledges who have trained their whole lives for this one thing, but she has … something special that causes her to win. Also archery is her greatest skill, and she's already awesome at it from the beginning of the story and never spends time practicing.
Close-but-not-perfect examples of the right thing:
The Pillars of the Earth - Jack pretty explicitly has to travel around Europe to acquire the skills he needs to become great. Much of the practice is off-screen, but it's at least a pretty significant part of the journey.
The Honor Harrington series: the books depict Honor, as well as the people around her, rising through the ranks of the military and gradually levelling up, with emphasis on dedication to training, and that training is often depicted onscreen – but the skills she's training in herself and her subordinates aren't nearly as relevant as the "tactical genius" that she seems to have been born with.
I'd like to put out a request for fiction that has this quality. I'll also take examples of fiction that fails badly at this quality, to add to the list of examples, or of TVTropes keywords that would be useful to mine. Internet hivemind, help?