One reason could be Naruto's unwavering determination. He has always been able to push past his limits. In many battles, his willpower has been a key factor in his victory. Another could be his unique chakra nature and the amount of chakra he has at his disposal. Naruto has a vast reserve of chakra, which gives him an edge in long - drawn battles. Also, his ability to form strong bonds with others might contribute. These bonds could potentially unlock new powers or give him the strength to fight against Kaguya.
Well, Naruto has had the advantage of learning from many great shinobi over time. He also has a unique bond with his friends which could potentially give him more strength. Minato, on the other hand, had a shorter lifespan to develop his powers. Naruto has had more time to grow and surpass his father in strength.
In fanfiction, Naruto can be stronger than Madara for multiple reasons. Some authors might want to subvert the expectations set by the original story. They could give Naruto unique abilities like the ability to manipulate time, which would clearly put him above Madara in terms of power. Additionally, it could be a way to bring in crossovers. For instance, if Naruto gains powers from another fictional universe, he could easily be made stronger than Madara. Moreover, the author may simply want to explore a scenario where Naruto is the most powerful character, and making him stronger than Madara is a step towards that.
One reason is Naruto's vast chakra reserve. His Uzumaki heritage gives him an almost unlimited supply, which can be emphasized more in fanfic. So he can keep going in a fight longer than Kakashi.
One reason is that Naruto has the Nine - Tails' chakra. In fanfic, this power can be further enhanced or manipulated in ways that make him far more powerful than Sasuke. Another reason could be his more outgoing personality. He might be able to form alliances more easily, leading to him having more resources and power - ups at his disposal.
Often, in fanfic, Naruto is made stronger than Itachi because the writers want to explore new story arcs. If Naruto is stronger, new and exciting battles and relationships can be created. For instance, Naruto could be the one to protect Sasuke from Itachi in a different way. Also, Naruto's positive and determined nature makes him a popular character to be super - powered in fanfics.
One reason could be the variety of his abilities. Naruto has a whole range of jutsu like the Rasengan and Shadow Clone Jutsu. In fanfiction, these could be made extremely powerful. For instance, if his clones could multiply infinitely and each had the power of the original, that would be a huge advantage.
One possible reason could be that Naruto has developed some new and extremely powerful jutsu in the fanfiction. Maybe he has found a way to combine his Sage Mode with his Kurama chakra in an even more efficient and powerful way that gives him an edge over Madara.
One possible reason could be that Naruto has access to some new and powerful jutsu. Maybe he discovers a secret family technique or is taught by a very powerful sage. This new knowledge gives him an edge over Kakashi.
One reason could be a new magic source. Natsu might discover a powerful magic that surpasses Gildarts' abilities.
One reason is his Nine - Tails chakra. It gives him a huge power boost that Jiraiya doesn't have. Another is his ability to learn quickly. Naruto has shown throughout the series that he can pick up new jutsu fast.