It could be an original character created specifically for the fanfiction. Maybe a rogue ninja with a vendetta against the Hidden Leaf Village.
Sasuke could potentially be the main character in a 'naruto cold killer' fanfic. He already has that brooding and somewhat cold personality. In this fanfiction, he could take his thirst for revenge to an extreme level and become a cold - blooded killer, hunting down those he believes are responsible for his clan's massacre. This would be a very different take on his character compared to the original Naruto story.
It could be a long - lost Uchiha clan member who has a killer instinct amplified by a dark jutsu. This character has a vendetta against the Hidden Leaf for past wrongs done to the Uchiha. They use their Sharingan in very cruel ways, not hesitating to kill even innocent bystanders to achieve their goals.
It could be an ordinary person who has been pushed to the edge. For example, a young man who lost his family to a powerful and corrupt group and decides to take matters into his own hands.
As we don't have much information about this fanfic, it could be this 'kiraai killer' is the main character. But it's also possible that Naruto or one of the other main Naruto series characters still take the lead role while the 'kiraai killer' is a secondary but important character.
Maybe Jiraiya. He's a pervy sage in Naruto, but if he were to cross over into the Fairy Tail world, his skills as a ninja, his knowledge of various jutsus, and his mentoring abilities could be applied in really interesting ways. He could mentor some of the younger Fairy Tail mages and teach them unique combat techniques.
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.
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.