Sasuke could be an interesting main character for this kind of fanfiction. His thirst for power and his complex relationship with the ninja world could be further explored if he were to become the Shadow Monarch. He might use the power to reshape the ninja world according to his own vision.
Kakashi could also be a great choice. His experience and wisdom would play a crucial role if he were to inherit the Shadow Monarch powers. He could use it to mentor a new generation of ninjas while also dealing with the threats that come with such a powerful ability.
It could be an original character. For example, a young orphan ninja who has always felt like an outcast in the village. Discovering the Shadow Monarch powers gives them a new sense of purpose and a chance to prove themselves.
One idea could be a crossover where the Shadow Monarch's powers are introduced into the Naruto world during a major conflict, like the Fourth Great Ninja War. The main character, perhaps a young ninja, discovers the power of the Shadow Monarch and has to learn to control it while also dealing with the existing political and power struggles in the ninja villages.
It could be a rogue ninja who has a special ability to disrupt shadow clones. This antagonist might be jealous of Naruto's ability to use shadow clones for training and wants to stop him. Maybe he has a jutsu that can make Naruto's clones go berserk and attack him instead of following his commands.
It could be an evil shinobi who has somehow harnessed shadow dragon slayer magic for his own evil purposes. He uses it to create chaos and destruction in the ninja world, and Naruto and the dragon slayer have to stop him.
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 Naruto's son or daughter. They would be a natural choice as they inherit Naruto's bloodline.
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.
It could be an original character created specifically for the fanfiction. Maybe a rogue ninja with a vendetta against the Hidden Leaf Village.
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.