Naruto is definitely one of the most popular. His journey from an outcast to a hero provides a lot of material for fanfic writers. Sasuke is also very popular as his complex character and his relationship with Naruto are always interesting to explore. Hinata is quite popular too, especially in fanfics that focus on her love for Naruto and her own growth as a ninja.
One of the most popular is 'Naruto Shippuden: Sakura Hiden - Thoughts of Love, Riding Upon a Spring Breeze'. It's popular because it shows Sakura in a new light, with her own adventures and growth.
Naruto is likely to be one of the main characters as he is the protagonist of the Naruto Shippuden series. He would probably be central to any fanfiction set in this universe. Sakura might also be there, as she is one of Naruto's closest friends. And depending on the plot, characters like Minato (Naruto's father) who has a connection to the events in The Lost Tower could be a main character as well.
Madara Uchiha is very important. He is behind many of the events that unfold in the Naruto Shippuden full story. His grand plan to reshape the ninja world and his immense power make him a formidable foe. His backstory also helps to explain a lot about the history of the ninja world and the Uchiha clan.
Minato's character could be developed by showing his growth from a young, talented ninja to a more mature and responsible leader. His relationship with Kushina can play a big part in this. For example, through his love for her, he becomes more empathetic. Kushina, on the other hand, could be developed by exploring her past and how it affects her actions. Her time with Minato helps her become more confident and less impulsive.
The First Hokage is obviously the main character. But we may also see other important figures like his contemporaries, who were also involved in the establishment of the Hidden Leaf Village.
I don't think it's strange at all. Naruto is a very curious person. Fanfiction can offer new perspectives on his own life and the lives of his friends. He might learn something new about himself or get inspired by the creative ideas in the fanfiction. It could also be a form of entertainment for him during his downtime.
A Naruto x Hinata fanfiction could focus on a mission they go on together during Naruto Shippuden. They are forced to rely on each other in a dangerous situation. Hinata gets injured protecting Naruto, and Naruto is filled with a new - found determination to protect her. This experience deepens their bond, and Naruto starts to see Hinata in a whole new light, leading to the start of their romantic relationship.
Another interesting novel is 'Naruto Shippuden: Kakashi Hiden - Lightning in the Icy Sky'. It focuses on Kakashi's story and his past, which is really fascinating. There are a lot of details about his relationships and his growth as a ninja.
Well, Kurama's sad story in Naruto Shippuden is complex. He was feared by the villagers in the Hidden Leaf because of his power. When he was sealed into Naruto, he was angry and tried to take over Naruto's body multiple times. His past was filled with being hunted and then trapped. It wasn't until he started to understand Naruto's will and dreams that he began to change. Naruto's unwavering determination and kindness towards him slowly melted his cold heart.