Perhaps the main antagonist could be a powerful and corrupt ninja from another village. This ninja is trying to take over all the ninja villages and create his own empire. Naruto, not being a jinchuuriki, would need to unite the other villages in a different way, relying on his charisma and his ability to inspire rather than his tailed - beast - related strength. This would change the power dynamics and the overall narrative of the story.
Another option is that an ancient ninja clan that was thought to be extinct resurfaces. They oppose the current ninja system and see Konoha as a symbol of everything they dislike. Naruto, without his jinchuuriki powers, would have to figure out a way to use his wits and the help of his friends to stop this new threat. This would make for a very different kind of story compared to the original Naruto plot where the jinchuuriki powers often played a major role in battles.
It could be a rogue ninja who has a vendetta against Konoha for some past wrong. Maybe he was once a Konoha ninja but was wrongly exiled and now wants revenge. Without Naruto having the jinchuuriki power, this antagonist would pose a different kind of threat as Naruto would have to rely on his other skills to face him.
Maybe Danzo. He's always been a power - hungry character. In a story where Naruto doesn't have the jinchuuriki advantage, Danzo could see it as an opportunity to take over the village without the threat of Naruto's special power standing in his way.
One possibility could be that Naruto focuses more on mastering unique ninja techniques that are not related to the power of the tailed beasts. For example, he might delve deeper into his wind - style jutsu and create new and powerful variations.
One possible unique storyline could be Naruto focusing more on his pure ninja skills without the power boost from being a jinchuuriki. Maybe he'd develop his own special jutsu that are not related to the tailed beast's chakra.
He might develop more self - reliance. Without relying on the power of the tailed beast, Naruto has to work harder on his own training. He could become more strategic in battles as he doesn't have the brute force of the jinchuuriki to fall back on.
The Jinchuuriki's mentors or those who protect them could also be main characters. For instance, Kakashi could be a main character in a fanfiction where he is tasked with training a new Jinchuuriki. His experience and wisdom would play a crucial role in the Jinchuuriki's development, and his interactions with the other characters in the village would add depth to the story.
It could be an original character created by the fanfiction author. This would give the author a lot of creative freedom to shape the character's backstory, personality, and abilities in relation to being the jinchuuriki of three.
The other Jinchuurikis could be potential allies. They understand the struggles and the power that comes with having a tailed beast inside them. For example, Killer Bee, who has a good relationship with his tailed beast, could share his insights on how to better co - exist with Shukaku. Tsunade might also be an ally, as she is a powerful Hokage who could offer protection and resources to the Jinchuuriki.
It could be Orochimaru. He has always been interested in power and the secrets of the tailed beasts. So, he might see Naruto and the Jinchuuriki family as a source of great power to experiment on or steal from.
It could be someone from the Naruto universe who doesn't like Naruto's newfound fascination with Aku. For example, Danzo might see Naruto's interest in Aku as a threat to the stability of the village and try to stop Naruto from further exploring Aku - related things. So, Danzo could be the main antagonist in this case.
Maybe a new character could be introduced as the main antagonist. This character could be from a hidden village that has been secretly observing Naruto's growth. They realize his potential as a weapon and plan to steal his power or use him to start a war against other villages.