It could be an adult who had a very difficult childhood and is given a chance to go back and rewrite it. For example, a character who grew up in poverty and now gets to experience a better childhood.
Perhaps a character who has just gone through a major life change or trauma. Going back to being a kid could be a form of escapism for them. They would be the main character, trying to make sense of this new (old) world and figure out how to deal with their present - day problems through the lens of their childhood.
Naruto himself could be a great crossover character. Since Kakashi is his mentor in the original series, seeing them interact when Kakashi is a kid could be really interesting. They could have a different kind of dynamic, with Naruto perhaps being the more experienced one in some aspects. Another potential character is Goku from Dragon Ball. The contrast between Kakashi's ninja skills and Goku's martial arts and superpowers would create a really exciting crossover.
Maybe a scientist who, in the pursuit of a dangerous experiment, has a brush with death and then has to deal with the consequences. This character could be very intelligent but also a bit reckless.
Sora could be a main character as he is often central in the Keyblade universe. His determination and pure heart would make him a key figure in the war. Another could be Riku, with his complex character and his own journey of growth and redemption.
A new, original character could be the main character in a Naruto chains fanfiction. This character could be from a small, unknown ninja village and possess a unique ability to control chains made of some special material. They could come to the Hidden Leaf Village and get involved in the events there, interacting with the well - known Naruto characters.
A fallen angel could be a great main character. They have already experienced a fall from grace and now are faced with these 108 earthly temptations as a chance for redemption. They have knowledge of both good and evil, but still struggle with the earthly allures.
Obviously, the drunk dragon itself can be the main character. It could have a unique personality, perhaps being a bit clumsy and overly friendly when drunk.
Obviously, the black wolf itself could be a main character. It could have a distinct personality, like being brave yet a bit solitary.
The protagonist from the original work can be a main character. For instance, if it's a fanfiction based on a superhero story, the superhero could be the main character who changes their tactics. Maybe they stop relying on their superpowers all the time and start using their intelligence more. Another potential main character could be a sidekick who steps up and changes their tactics to fill in when the hero is incapacitated. For example, they might start using some of the hero's gadgets in a different way than the hero does.
A young girl who has always been fascinated by Sakura could be a main character. She might be on a journey to see the most amazing Sakura blossoms.
A powerful sorcerer or priestess who has a lot of influence over the religious and magical aspects of Babylon could be a main character. They could be involved in political intrigues as they try to use their powers to further their own agendas or protect the kingdom. Another potential main character could be a foreign diplomat who comes to Babylon and gets caught up in its complex web of power and politics.