Perhaps Sasuke could be the main character in this fanfiction. Given his complex relationship with the idea of death and resurrection in the original Naruto story, having the reanimation eyes would add another layer to his character arc. He could use the eyes to try and bring back his clan or seek revenge in a new way.
It could be a new character. Maybe an orphan who discovers they have these reanimation eyes and has to figure out how to use them while also dealing with the fact that they are different from everyone else in the ninja world.
Well, in 'naruto reanimation eyes fanfiction', a cool concept might be the connection between the reanimation eyes and the afterlife. It could be that the eyes are a link to the souls of the dead, allowing the user to communicate with them or even bring them back in a more complete form than normal reanimation jutsu. This could lead to all sorts of plot twists and character development.
It could be an original character created specifically for this fanfiction. Maybe a young ninja who discovers they have these cursed eyes and the power of prophecy unexpectedly.
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.
It could be a new student at Hogwarts. A young witch or wizard who discovers they have the Eyes of Merlin and has to deal with the sudden power and the attention it brings from both good and bad forces.
In fanfiction, the reanimation jutsu might have extended or modified limitations. For instance, in the original, there were clear rules about the caster's control over the reanimated. But in fanfiction, a writer could create a scenario where the reanimated can break free of that control more easily. Also, the source of the sacrifice for the jutsu could be different. In the series, it was usually human sacrifices, but fanfiction might explore using other forms of energy or substances.
One common theme is redemption. The reanimated characters often get a chance to right their past wrongs. Another is the exploration of old relationships. Since they come back, they can re - interact with their former friends or foes.
It could also be a young apprentice of the shopkeeper. This character could be learning the ropes of running the shop while also having dreams of becoming a great ninja. They would be in a position to interact with both the regular customers of the shop and the more famous ninjas, which could lead to all sorts of interesting storylines.
It could be Megaman himself. He could be transported to the Naruto world and have to adapt to the new environment while using his skills to make a difference. His sense of justice would fit well in the Naruto universe.
It could be an original character created specifically for the fanfiction. Maybe a rogue ninja with a vendetta against the Hidden Leaf Village.
Naruto himself could be the main character. Imagine Naruto getting his hands on a special pistol - like weapon and having to learn how to use it while still relying on his normal ninja skills. It would be a new challenge for him and could lead to some great character development as he tries to master this different form of combat.