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 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.
Often, the main protagonists from the major clans are popular. For instance, the leaders of the Uchiha and Senju clans tend to be popular as they play significant roles in the clan wars. Their unique abilities and complex personalities make them interesting to write about.
A young, orphaned shinobi with no known clan but extraordinary skills. He could be a wildcard in the clan wars, not bound by traditional clan loyalties.
It could be an older, wiser shinobi who has seen many things in the shinobi world. He might be guiding the younger members of the kekkei clan and be a central figure in the story. There could also be an antagonist, maybe from a rival clan, who is constantly trying to undermine the kekkei clan shinobi's efforts.
One idea could be a story about an underdog shinobi from a small clan who discovers a hidden power within himself during the clan wars. This power could be the key to uniting the clans against a common, greater threat that has been manipulating the wars from the shadows.
There could be some original characters created specifically for the fanfic. For example, a young shinobi from a small village who has a unique power related to nature. This character could have a significant role in the Shinobi Wars, perhaps by forming an unexpected alliance with Naruto and his group. Their journey together, with the new character learning from Naruto and growing, would make them a memorable part of the fanfic.
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.
An older, retired shinobi who is forced to come out of retirement during the shinobi wars. He has old - fashioned techniques but a wealth of experience. He could mentor a group of young shinobi and help them develop new strategies based on his years of combat knowledge.
I'm not sure specifically as it depends on the fanfiction. But it could be new characters created as a result of the clan fusions, like a character who is part Uzumaki and part Nara, with unique abilities from both clans.
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.