It's possible that a group of students could be the main characters. They all learn from the genius sensei in different ways. One student might be great at physical combat, another at ninjutsu, and they have to work together under the sensei's guidance. Their combined growth and how they interact with each other and the sensei can form the core of the 'naruto genius sensei fanfic'.
Obviously, Naruto himself would be one of the main characters as he is the sensei. His students could be a group of new genin. For instance, the children of his old friends like Boruto and Sarada could be among his students.
Orochimaru is another possibility. He is already somewhat of an evil genius in the original Naruto series. In a fanfiction, he could be further developed as the main character, perhaps with his experiments taking on even more extreme and far - reaching consequences. His actions and plans could be the central focus of the story, with other characters either trying to stop him or being caught up in his schemes.
One interesting concept could be how the genius sensei in the fanfic imparts unique ninja skills to the students. For example, they might introduce new jutsu combinations that are not seen in the original Naruto series. This can add a fresh perspective to the Naruto universe.
For Naruto, he would likely gain a new level of understanding about the Uchiha. His view of the Sharingan and the power it holds might change. He could also develop a more nuanced approach to dealing with enemies, as Mikoto might teach him some of the Uchiha's battle strategies.
A likely main character could be a young ninja who discovers he has the 'One for All' power. He would be on a journey to understand and control it, while also dealing with the normal challenges of being a ninja in the Naruto world, like training and making friends.
Naruto himself could also be a main character. He could visit the Hidden Star Village and interact with the Hoshikage, getting involved in the village's affairs and helping them solve their problems. This would be an interesting way to incorporate the Naruto we all know into the fanfic.
The main themes often include friendship and inspiration. Gai Sensei is such an inspiring character, and in these fanfics, his relationship with Naruto is based on mutual respect and friendship. Also, the theme of perseverance is prominent. Gai Sensei's unwavering perseverance in his own ninja way is passed on to Naruto, and we see Naruto face challenges with that same tenacity in the fanfics.
One potential main character could be a young Iburi Clan member who is just starting to come into their powers. They would be full of enthusiasm and curiosity about their clan's abilities. Another could be an older, more experienced Iburi Clan ninja who has seen a lot and is now a mentor figure. And then there could be a half - Iburi Clan character, who struggles with fitting in both the Iburi Clan world and the world of their other heritage.
Obviously, Naruto would be one of the main characters. Since he is the son of Khal Drogo in this fanfic, he would be central to the story. Another potential main character could be Sasuke. His relationship with Naruto could be even more complex now, as Naruto has this new and strange heritage. And maybe one of Khal Drogo's most trusted warriors could also be a main character, coming to the Naruto world to help Naruto understand his father's side of the family and teach him things about his newfound heritage.
Boruto, Naruto's son, is an obvious choice. He already has his own story in the Boruto series, but in a fanfic, you can take his character in new directions. Himawari, Boruto's sister, could also be a main character. She has the potential for great power and a unique personality.