Kakashi could also be the main character in a different take on 'naruto rogue ninja fanfiction'. Imagine if for some reason, Kakashi was framed as a rogue ninja. He would have to use his intelligence and combat skills to clear his name while also dealing with the challenges of being an outcast. He might even discover some dark secrets about the Hidden Leaf Village in the process.
The Leaf Village authorities could be the main antagonists. Since Naruto is now considered a rogue, they would be the ones trying to hunt him down. They might see him as a threat to the village's stability and security.
It could be a group of rogue ninja who have a vendetta against Naruto. They might see his new status as a rogue as an opportunity to take him down. Maybe they were once defeated by Naruto when he was in the village, and now they want revenge. Also, there could be some hidden shinobi clans within the village who oppose Naruto's new path and try to stop him for their own reasons, like protecting the village's reputation or their own power within the village.
It could be Naruto himself. Imagine Naruto encountering a rogue Shinigami and having to deal with the chaos it brings. He would be the perfect main character as he is always eager to face challenges and protect his friends and the village.
It could be a new character, an ice ninja named Hakuji. He has a tragic past, his family was killed by a rogue ninja group and he was left alone in the cold northern lands. He comes to Konoha seeking revenge at first but then befriends Naruto and changes his path.
Shizune. She was Tsunade's assistant and a very capable medical ninja. A fanfic could focus on her backstory, like how she became a medical ninja and her experiences during the various battles she was a part of. She could also have her own adventures away from Tsunade.
It could be an original character. For instance, a ninja from a small, unknown village who has a unique power and is forced to participate in the war. They could be the underdog that everyone underestimates at first.
Well, one possibility is that Naruto feels betrayed by the Hidden Leaf Village. Maybe they wrongly accused him of a serious crime. So, he decides to go rogue. He could then start traveling alone, using his skills to survive and avoid capture. He might also meet other outcasts who understand his situation.
Sasuke is often a popular character in these fanfics. His own stint as a sort of rogue ninja makes him a natural fit. Also, Orochimaru, who was a rogue ninja for a long time, is frequently included. He has a lot of mystery and power associated with him.
The Hidden Leaf Village itself could be the main antagonist. If they turn on Naruto for no good reason, they become the force he has to fight against as a rogue ninja.
Another possibility is that the main antagonists could be the leaders of the other ninja villages. They might view Naruto's godlike and rogue status as a danger to the balance of power among the villages. So, they could form an alliance against Naruto, leading to a lot of political intrigue and conflict in the story.