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 could also be the main character. Imagine if he encounters Megaman and is intrigued by his technology. He might try to learn from Megaman and incorporate some of his ideas into his own ninja way, leading to a new level of power for Naruto.
Zero himself could be the main character in a sense. Imagine he somehow gets transported to the Naruto universe. He'd be a fish out of water at first, but his combat skills and sense of justice would make him a force to be reckoned with. He could start to learn about chakra and ninjutsu, and use his knowledge from his own world to help or even lead the Naruto characters in battles against new threats.
Dr. Wily could be the main villain. He might have found a way to travel through time or dimensions to the world of Mega Man X. He then uses his knowledge of Mega Man's weaknesses and combines it with new technology in the Mega Man X world to create even more powerful and devious robots.
It's really hard to say. Naruto has his powerful jutsu like the Rasengan and his ability to use the Nine - Tails' chakra. But Megaman has all those different weapons and upgrades. If it was a long - distance battle, Megaman might have the edge with his blaster. But in close - quarters combat, Naruto could use his taijutsu skills. So it really depends on the situation.
A likely main antagonist could be a rogue scientist who has found a way to merge the technologies from both the Megaman Star Force and Megaman X worlds in a very dangerous way. He wants to use this new power to take over both universes.
A new character could be introduced as the main antagonist. For example, a being from another dimension who has been observing both Sonic's and Megaman's worlds. This being realizes that by combining the chaos energy from Sonic's world and the advanced robotics technology from Megaman's world, it can create a new, all - powerful empire. So it starts to manipulate events in both worlds to bring about this combination, while Sonic and Megaman have to stop it.
Dr. Eggman and Dr. Wily could team up. Dr. Eggman has his mechanical creations and knowledge of Sonic's world, while Dr. Wily is an expert in creating powerful robots in Mega Man's world. Together, they could be a formidable force against Sonic and Mega Man.
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 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.