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.
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 a new character created by the fanfic writer. Maybe a young orphan who discovers their seal - making talent by accident.
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.
One option for the main antagonist could be a secret organization that has infiltrated Konoha. They target the Anbu prodigy because they fear the prodigy's abilities could expose their existence and plans. This organization might have members with unique and dangerous abilities themselves. They would constantly send assassins after the prodigy and try to create chaos in Konoha to keep the Anbu and the prodigy distracted while they carry out their real objectives.
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.
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.
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.
The obvious main character would be the neglected Anbu prodigy. He could be someone with a tragic past that led him to the Anbu in the first place. Another important character could be Naruto himself. Even though it's about the neglected prodigy, Naruto's presence is what causes the neglect, so he would play a significant role in the story.