Another option could be a completely new character, a young orphan shinobi who has no clan but tries to survive and make a difference during the clan wars. This character could have unique abilities or a special motivation that drives them to get involved in the clan conflicts. They could form unexpected alliances and discover secrets about the clans along the way.
A good choice could be a young Itachi Uchiha. He was a prodigy even at a young age, and his story during the clan wars era could be really interesting. He was torn between his loyalty to the Uchiha clan and his understanding of the bigger picture in the village.
Perhaps a member of the Inuzuka clan. They are known for their loyalty and their unique abilities with their ninja dogs. A story following an Inuzuka shinobi's journey through the clan wars, facing challenges, and forming alliances with other clans would be engaging. You could also consider a young Kakashi Hatake. He had a complex backstory, and his experiences during the clan wars era could be explored, especially his relationship with his father and how that was affected by the wars.
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.
It could be a young Naruto Uzumaki, exploring his family's past during the clan wars era. He might discover secrets about the Uzumaki clan that have been long forgotten.
Sasuke Uchiha would be an obvious choice. He's a central Uchiha character in the Naruto series. His journey to avenge his clan and his complex relationship with the rest of the Uchiha could be further explored during the clan wars. Another could be Itachi Uchiha. His actions and the secrets he held were crucial to the Uchiha's situation, and in a fanfiction about the clan wars, his role could be even more in - depth.
Obviously, Naruto is one of the main characters. He is usually at the center of the story, using his skills and determination to navigate the clan wars. Sasuke is also often a main character, as his past and connection to the Uchiha clan play a big role. Sakura might be there too, using her medical ninjutsu to help those injured in the wars. And then there are the clan leaders, like the Nara clan leader or the Hyuga clan leader, who have their own agendas and power dynamics within the story.
Naruto himself could be a main character, using his skills and influence to try and stop the clan wars. Another could be a young shinobi from a minor clan who has a special ability and wants to prove their clan's worth. And Sasuke could also be involved, perhaps having his own motives related to the clans.
It could be a group within Naruto's own clan who have turned against the rest of the clan due to some ideological differences. They might want to use the clan wars as an opportunity to take over the clan and change its values. Another possibility is a mysterious and powerful ninja from another land who has his own motives for causing chaos during the clan wars.
Obviously Naruto Uzumaki himself. He is the central figure of the Naruto series and with the focus on the Uzumaki clan wars, he would be right in the middle of it all, using his skills and the power of the Uzumaki bloodline.
A female shinobi who defies the traditional gender roles in her clan during the wars would make an interesting main character. She could break barriers and show that women can be just as powerful and important in the shinobi world as men, and her actions could have a significant impact on the outcome of the clan wars.
Naruto is the central figure for sure. But there could be other Uchiha characters like Shisui who could be involved. Shisui was known for his loyalty and strong will. He could befriend Naruto and help him adjust to the Uchiha way of life. And of course, the clan leader at the time of Naruto's adoption would also be a key character, making decisions about Naruto's place within the clan.
The clan leader of the Badger Clan is likely to be a main character too. They would be responsible for making important decisions for the clan, like whether to get involved in the outside ninja world's affairs or to stay hidden. Their wisdom and leadership skills would play a crucial role in the story.