Predictably, Naruto turns out to have inherited all his abilities from his parents, and then improved on them only because he was possessed by the ancient spirit of one of the most powerful beings in existence. And even before that, when the story required him to be the underdog hero, he tended to overcome obstacles using the Kyuubi.
All of the Narutoverse in general is about magic powers (chakra, whatever) passing on from parents to children without much of a change. There's exactly one character in all of Narutoverse who's called out for being powerful due to training, and it isn't Naruto. (A few others are powerful due to research, which is of course always evil.)
Naruto is the opposite of Tsuioku Naritai. It's the story of "everyone had something to protect and practiced like mad, but none of it made a huge difference and most everyone would have been about as powerful anyway." Naruto climbs trees (metaphorically speaking) for many chapters, but keeps being the underdog. Then he starts manifesting powers that make him the most powerful individual in the universe - because he's a shonen hero - and which are entirely due to his parents and outside intervention.
Naruto is the opposite of Tsuioku Naritai. It's the story of "everyone had something to protect and practiced like mad, but none of it made a huge difference and most everyone would have been about as powerful anyway
But the series clearly wants to be "Tsuioku Naritai". The good guys all value hard work. Maybe the show is hypocritical, then.
I'm not sure if the message that sticks with the people who watch Naruto is what the characters say (work hard) or how the show actually develops (be born special).
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?