Sasuke could be a great main character for such a fanfiction. He's always been interested in power and knowledge. He might start his own experiments to gain more power, especially after his experiences with Orochimaru.
Kakashi could be an interesting choice too. He's a very intelligent and experienced ninja. He might be conducting experiments in secret to find ways to counter new threats in the ninja world. His knowledge of various jutsus and ninja techniques would make him a great experimentor in a fanfiction.
One idea could be exploring new jutsu experiments. For example, a character tries to combine different elemental jutsus in a way that's never been done before. This could lead to unexpected powers and consequences.
It could still be Naruto himself, just with a focus on a different, smaller part of his life or personality.
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.
Naruto himself could still be the main character. He might be faced with a situation where he has to make difficult choices to prevent carnage, and in the process, his character could develop in new and unexpected ways, like having to use more ruthless tactics.
A new character could be the main character in a 'naruto ambassador fanfiction'. For example, a young ninja who was inspired by Naruto's story and trained hard to be like him. This new character could be given the role of ambassador to show how Naruto's influence has spread even to the newest generation of ninjas, and they could bring a fresh perspective to the diplomatic table.
Rock Lee could be a great main character. He's known for his physical strength and determination. With the Kabutowari, he could develop new fighting styles that combine his taijutsu skills with the power of the weapon. For example, he could use it to break through an opponent's defenses during a high - speed taijutsu battle.
It could be Naruto's son or daughter. They would be a natural choice as they inherit Naruto's bloodline.