Obviously Naruto himself would be a main character. He could bring his unique ninja skills and his determination to the story. Another could be Noctis from Lucis Caelum. His powers and his role as a prince could add a lot of drama and action to the fanfiction.
Sakura could also be a main character in this fanfiction. She might be the one who first discovers the link between the two worlds due to her medical knowledge and her intelligence. And from Lucis Caelum, Prompto could be a main character. His cheerful nature could contrast with the more serious Naruto characters at times.
A really interesting plot could be that the ninjas in Naruto's world start to have dreams about Lucis Caelum. These dreams seem to be prophetic, and Naruto decides to investigate. Along the way, he meets a character from Lucis Caelum who helps him decipher the meaning of these dreams and together they try to prevent a disaster that is predicted to occur in both worlds.
One great Noctis Lucis Caelum time travel fanfiction is 'A Journey Through Time'. It has an interesting plot where Noctis travels back to key moments in the history of his kingdom. The author does a great job of portraying how Noctis reacts to the past events and how his actions in the past might change the future.
The theme of self - discovery is also quite prevalent. In a new time period, Noctis has to re - evaluate who he is and what his purpose is. For example, in some fanfictions, he sees how his family's actions in the past shaped who he is in the future. And the theme of sacrifice often comes up. He may have to sacrifice something in the past to ensure a better future for his kingdom.
Obviously Naruto and Sasori. Naruto as the'son' would be the central figure in terms of the story's development. And Sasori, as his 'father' in this fanfiction, would play a crucial role in shaping Naruto's growth.
One potential main character could be a new ninja who discovers they have the Ink Release. They are an outcast in their village at first because of this strange power but then learn to master it and become a hero. For example, a young orphan who is bullied for having this unusual ability.
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.
Naruto and Shinso are the primary ones. But we could also have an old and wise vampire elder as a main character. This elder could have knowledge about a prophecy that involves Naruto and Shinso, and his actions and decisions would drive a lot of the plot as he tries to either fulfill or prevent the prophecy.
A potential main character could be a long - lost relative of Hashirama who has the mokuton ability but has been neglected in the main Naruto story. This character could then embark on a journey to discover their true power and place in the ninja world.
Obviously Naruto would be the main character since it's about him being reborn as a Pokemon fan. His Pokemon partners could also be considered main characters. For example, a Pikachu that he befriends early on and they go on adventures together.
It might also be possible for new characters to be the main characters in this fanfiction. For example, a young ninja who discovers a Keyblade and has to learn how to use it while also dealing with the politics and power struggles in the Naruto universe. They could be from a minor clan but rise to prominence through their Keyblade skills.