It could be an Uchiha who has turned against the clan. Maybe an Uchiha who is jealous of Naruto suddenly having Uchiha powers and wants to take them away or prove that he's the true Uchiha prodigy. This could create a whole new internal conflict within the Uchiha clan.
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.
Another possibility is that Orochimaru could be the main antagonist. He's always been interested in powerful ninja and unique abilities. Naruto's new Uchiha powers would be very appealing to him, and he might try to use Naruto for his own evil experiments or to gain more power in the ninja world.
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.
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.
Maybe an entire rival village decides to target the prodigy. They see the potential threat that the prodigy poses to their own village's dominance, so they send their best ninjas to take the prodigy down.
A new character could be created as the antagonist. For example, an Uchiha who has been corrupted by the power of the Sharingan and wants to use Naruto's special Uchiha - related abilities for his own evil purposes. This character could be jealous of Naruto's unique position within the Uchiha - related story and try to take it from him.
It could also be a member of the village leadership who has a deep - seated prejudice against the Uchiha. This person is constantly trying to undermine the Uchiha's position and is willing to start and fuel the wars in order to get rid of them. They see the Uchiha as a threat to the stability of the village.
In a 'naruto the uchiha prodigy fanfic', the main focus would be on the Uchiha prodigy. But considering the context of the Naruto universe, there would be a whole host of other characters involved. Naruto would most likely be present, as his story is intertwined with the world of the Uchiha. Sakura could also be part of the story, perhaps as a healer or a friend to the Uchiha prodigy. And then there are the villains from the Naruto series. Orochimaru, for instance, might be interested in the powers of the Uchiha prodigy and try to manipulate or use them for his own purposes. So, the main characters would be a mix of the Uchiha prodigy, Naruto - related characters, and potential antagonists.
It could be Madara. Even if Obito goes back in time, Madara's long - term plans for the ninja world are still in motion. He might be the main force that Obito has to oppose as Madara's ideas often lead to destruction and chaos.
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.
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.