Sometimes, it might even be Naruto himself in an alternate universe where he is even more of a ninjutsu prodigy from the start. He could quickly master all the Hokage - level jutsus and become an even more powerful ninja at a younger age.
It could be an original character created by the fanfiction author. This character might have a special background or power that makes them a ninjutsu prodigy.
It could be a new character created by the fanfic writer. Maybe a young orphan who discovers their seal - making talent by accident.
Well, one common story could be about the character being a ninjutsu prodigy who quickly masters advanced jutsus that others struggle with for years. For example, they might develop a unique way to combine fire and wind jutsus in a more powerful form.
It could be someone like Rock Lee. He was a hard - working prodigy in taijutsu, but often got overshadowed by the more flashy abilities of others. Maybe in this fanfiction, he's completely forgotten until he does something extraordinary to get noticed again.
Perhaps it could be a new character created specifically for the fanfiction. A young ninja from a minor clan who showed extraordinary talent in a unique form of jutsu. But because their clan was small and not very influential, and the larger clans felt threatened by this new talent, they managed to get the village to abandon this prodigy.
There's also a chance that the main character could be a completely new character from a minor clan in the Naruto universe. This character could have some hidden bloodline limit that makes them a prodigy in the ANBU. They might start as an underdog but quickly rise through the ranks due to their exceptional skills and intelligence.
The Akatsuki could still be the main antagonists. Since Naruto now has Uchiha powers, they might be even more interested in him. They could see him as a threat or a valuable asset to their plans, just like they did with Sasuke.
There could be a group of ninjas who are in cahoots to keep Naruto in the shadows. They might see him as a threat to the current power structure in the village. They spread false rumors about him, or try to sabotage his training in subtle ways so that he remains an ignored prodigy. This group could be made up of some self - serving individuals who are only interested in their own status and power.
Sasuke could be a potential rival. He is highly talented and always striving to be stronger. His determination and different fighting style would make for an interesting contrast to the Nara prodigy.
Since it's a fan - made story, the main character could be anyone. It could be an OC (original character) designed to be the center of this forgotten prodigy narrative. They could have a backstory full of hardships that led to their being forgotten. Or, as I said before, it could be a familiar Naruto face but with a whole new story arc that focuses on their previously unacknowledged prodigious nature.
Perhaps it could be a relative of an existing character, like Neville Longbottom's younger cousin. Neville had his own growth in Herbology, so his cousin could be a prodigy in potions. They would have grown up in the same kind of environment where magic was a bit of a struggle at first, but then they find their true calling in potions and start to shine in that area.