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.
A foreign shinobi who comes to the Naruto world during the clan wars. He has different techniques and a different view on war, which could either help or hinder the situation depending on his motives.
A female shinobi from a newly discovered clan that has been hidden away for centuries. Her clan's unique abilities and culture could add a fresh perspective to the wars.
A shinobi from a hidden village that was destroyed long ago. This character could carry the secrets and unique jutsu of their fallen village and seek revenge or redemption in the Naruto world.
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 vampire scientist. This character could be researching ways to create a new type of vampire that is immune to the weaknesses of traditional vampires, like sunlight or silver. Their experiments could cause a stir among both the vampire and lycan communities.
Another plot could revolve around a young shinobi from a major clan who tries to prevent the wars by forging alliances between the clans. This would involve a lot of political intrigue and character development as they face opposition from within their own clans.
A mysterious shinobi from another village who has a connection to the ex - ANBU's past missions. This character could bring in new elements of foreign shinobi culture and different fighting styles.
A character who is a descendant of the original creators of the Fierce Diety form. This character could have knowledge about the form that Naruto doesn't and could either be an ally or an antagonist depending on their motives.
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.
Well, there could be his childhood friend who always believed in him. This friend might not be as strong in terms of combat skills but is very intelligent and helps him come up with strategies. There could also be an old hermit who lives on the outskirts of the village and imparts some ancient wisdom to the first male shinobi that gives him an edge in his battles.
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.