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.
In this fanfiction, Naruto could be stronger because of his growth in terms of experience and mental strength. He has been through many more difficult battles and challenges than Kakashi at this point. This has toughened his resolve and made him more in tune with his powers. He also might have made some unique alliances that provided him with special powers or resources, which Kakashi doesn't have.
Well, Naruto might have a stronger connection to his inner power in this fanfiction. His chakra control could be much better, allowing him to perform more powerful attacks and endure longer battles. He could also have trained in some special place or with unique creatures that enhanced his strength significantly.
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 a stronger willpower in the fanfic. His never - give - up attitude might be enhanced, allowing him to push past his limits more easily than Sasuke. For example, he might have an even deeper connection to the Nine - Tails' power, enabling him to draw on it more effectively in battles.
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.
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 possible reason could be that Kakashi is preoccupied with other important matters in the village. Maybe he has some top - secret missions or tasks assigned by the Hokage that demand his full attention, leaving him with little time to focus on Naruto.
One reason could be that he sees Naruto as a younger version of himself in some ways. Both have had their share of loneliness and challenges growing up. Kakashi may want to prevent Naruto from going through the same pain he did. Another reason is Naruto's importance to the village. As the jinchuriki of the Nine - Tails, Naruto is a key asset. Kakashi, being a loyal ninja, wants to protect the village's future which is tied to Naruto.
One possible reason could be that Naruto might feel Kakashi is too strict with his training. Maybe Kakashi's methods are too harsh for Naruto, making him frustrated and gradually developing dislike.
One possible reason could be Kakashi's reputation as a strict and powerful teacher. Naruto might be in awe of his skills and fear making mistakes in front of him.
One possible reason could be that Naruto might be trying to prove his independence. He has grown and wants to show that he can handle things on his own without always relying on Kakashi's guidance.
One reason could be that the fanfiction changes Kakashi's teaching methods too much. Naruto is used to Kakashi's unique style in the original story, and if it's drastically altered in a way that doesn't seem right to Naruto, he might not like it.