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.
Maybe a new character from a foreign land who enters the Naruto world with the 'One for All' power. This character would bring a fresh perspective, not being familiar with the ways of the ninja at first but quickly learning and adapting, all while trying to keep their power a secret from those who might misuse it.
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.
Well, of course, the main character is 'him'. But there could also be other important characters like his mentor who guides him on his journey. This mentor could be an old and wise figure who imparts valuable knowledge.
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 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.
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.
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.
Tsunade might also play a role. She could suspect Naruto of having a secret life and start an investigation. And of course, Orochimaru could be involved as well, either trying to use Naruto's secret for his own gain or being a part of the mystery that Naruto is trying to solve in his secret life.
Obviously Naruto as the main character. Sasuke could be there, and his relationship with Naruto might change due to Naruto's new identity. There could also be characters from the underworld, like minions of Hades or other mythological creatures.
Obviously Naruto himself. There could also be the other Naruto characters like Sasuke, Sakura, and Kakashi. And perhaps some Egyptian god - like characters related to Anubis, like his servants or other gods who interact with Naruto due to his relation to Anubis.
Obviously Naruto himself. Then there could be Athena, who might appear in some form, either as a guiding spirit or in flashbacks. His friends like Sasuke and Sakura would also be there. Maybe some Greek mythological characters like Hermes could show up to interact with Naruto, since he is now related to their world.