Aang from Avatar: The Last Airbender would be an excellent choice. Aang has the ability to bend all four elements, and his connection to the spiritual world could offer Naruto new perspectives on his own chakra. Another good one is Natsu from Fairy Tail. Natsu's dragon - slayer magic and his intense fighting spirit would make for an interesting training partner for Naruto. Additionally, Midoriya from My Hero Academia. Midoriya's analysis of his opponents and his own growth in power could be something Naruto could learn from.
Goku from Dragon Ball Z could be a great pairing. Both are powerful fighters who constantly strive to become stronger. They could have some epic battles to test each other's strength and then team up to face a powerful villain that neither could defeat alone. Goku's ki - based attacks and Naruto's ninjutsu would create some really cool fight scenes.
Sasuke is often a popular crossover character. His cool and brooding nature, along with his powerful Sharingan abilities, make him an interesting addition in crossovers. He could potentially team up with characters like Batman, given their similar dark and complex personalities.
In a crossover with Attack on Titan, Eren could be paired with Naruto. Naruto's immortality would give him an edge in the fight against the Titans. He could teach Eren some of his ninja techniques, like how to move stealthily. And Eren's determination to protect his people could be something Naruto relates to. They could work together to find a more permanent solution to the Titan problem, rather than just fighting them constantly.
Kakashi from Naruto himself could be part of a 'grey' themed crossover within the Naruto universe. Maybe a situation where Kakashi's past and his more mysterious side are explored further, and Naruto has to work with him in a darker, more complex mission that delves into the grey areas of the ninja world.
In this crossover, Naruto's Rasengan could be a powerful weapon against the zombies. He could spin through a group of zombies, taking them out in one go. Hinata's Byakugan could be useful for surveillance, being able to see in all directions and detect any approaching zombies long before they get close. Shikamaru, with his high intelligence, could come up with strategic plans to navigate through the zombie - infested high school, using the abilities of both the Naruto and Highschool of the Dead characters effectively.
Obviously Naruto would be one of the main characters. And from 'The 100', Clarke would likely be a main character as well since she is a central figure in her own show.
There might be some original characters created specifically for this fanfic. They could be characters that act as guides or rivals within the game - inspired aspects of the story. For example, a mysterious figure who gives Naruto quests or a fellow ninja who is competing with him for high scores in the game - like system.
One idea could be to have Naruto train with characters from other popular shonen series like Goku from Dragon Ball. They could exchange training techniques, for example, Naruto teaching Goku about chakra control while Goku shows Naruto how to better use his physical strength. Another idea is to have Naruto cross over with characters from Fairy Tail. The Fairy Tail mages could introduce Naruto to different types of magic-based training that he could incorporate into his ninja training. A third idea would be to have Naruto train with characters from One Piece. They could have a unique training session on a deserted island, learning survival skills from each other.
Definitely Naruto himself. His energetic and determined personality would be a great contrast to the often more somber characters in Skyrim. Also, characters like Sasuke could be interesting. His brooding nature and powerful Sharingan abilities would make for some great interactions in Skyrim's dangerous world. And from Skyrim, the Dragonborn would be a must - include. The clash or cooperation between the Dragonborn's Thu'um and Naruto's jutsu would be really exciting to write about.
For the Naruto side, Rock Lee would be really cool. His taijutsu - only fighting style could be really different from what the Halo characters are used to. In Halo, the Arbiter could be an interesting character to include. His story of redemption and his unique combat skills could lead to some great storylines. And of course, Hinata could also be included. Her shy but strong - willed nature could be a nice addition. She might befriend some of the Halo characters and learn new ways to fight from them.