Naruto himself could be the main character. Since he's the protagonist of the original series, it would be natural to have him as the center of the fanfiction. He could be drawn into the new game world and have to use his unique skills and determination to succeed.
Perhaps a young knight who is given a lordship as a reward for his heroism in a great battle. He is inexperienced in ruling but has a strong sense of justice. He has to learn quickly how to manage his lands, deal with political intrigue, and protect his people from bandits and rival lords. He is also a bit of a romantic, and his love interest could be a lady from a neighboring house, which adds another layer of drama to his story.
There's also a possibility that it could be an older character who has been forgotten or underestimated, like Rock Lee. He could have passed on his skills to a new generation but then has to come out of retirement to face a threat that only he can handle in this new dawn of the Naruto world.
It could be a new, previously unheard - of ninja who has the potential to become as great as the Yellow Flash. Maybe a young orphan who discovers some hidden power within themselves.
It could be an older and more powerful version of Orochimaru. In the new game plus scenario, he might have found a way to cheat death completely and has amassed an even greater army of experimental ninjas. He could be the main antagonist as he tries to take over the ninja world with his new - found powers and knowledge.
Sasuke could be the main character in a 'naruto new eyes fanfic'. Imagine Sasuke discovers a new evolution of his Sharingan that gives him additional powers. This could add a new layer to his character arc, as he struggles to come to terms with this new power and how it affects his relationships with Naruto and the rest of the ninja world.
Definitely, Gaara could be a central character. His control over sand could be the basis for some really cool transformations. Maybe he could transform into a giant sand creature or something more refined like a sand - armor form. Kiba with Akamaru could also be a main character. They could have a combined transformation where they become a more powerful and fearsome beast - like form. And Tenten could be a main character with a transformation related to her weapon - using abilities, perhaps a transformation that gives her an unlimited supply of weapons.
Madara Uchiha could be a great antagonist in this kind of fanfiction. He has the power and the ambition. He could manipulate the war game from behind the scenes, perhaps using his Sharingan to control the minds of some of the participants. He wants to reshape the ninja world according to his own vision, and the war game provides him with an opportunity to do so without directly confronting all the ninja forces at once.
I think Spider - Man would make an interesting main character. He's young and has a different perspective compared to the more experienced Avengers. His journey of growing up and becoming a more integral part of the team could be a central theme in the fanfiction. He also has his own set of personal problems like school and his relationships which could add depth to the story.
Perhaps a minor character from the original Fate series could be promoted to the main character. For example, a bystander in one of the battles who witnessed something extraordinary and was then drawn into the world of the Holy Grail War in a more central way in the 'a new fate fanfiction'.
It could be a rogue ninja who was once a part of Konoha but was banished for unethical experiments. Now, with a thirst for revenge against Naruto and the village, he returns as a powerful and unpredictable foe.