Cyclops could be a main character. His optic blasts might be seen as a very different kind of attack compared to the jutsu in the Naruto world. He could lead the X - Men in their interactions with the ninja clans. Naruto's friends like Sasuke could also be main characters. Sasuke's Sharingan and his complex personality would add depth to the story. He could be both intrigued and threatened by the X - Men's powers.
Obviously Naruto and Wolverine could be main characters. Wolverine's tough - guy attitude and his healing factor would contrast well with Naruto's upbeat and determined personality. Jean Grey could also be a main character. Her powerful telepathic and telekinetic abilities would be interesting to see in the Naruto world, especially when interacting with ninjas who rely on physical and chakra - based skills.
Storm would make a great main character. Her ability to control the weather could be a huge asset in the Naruto world, whether it's for combat or for helping the villagers. Naruto himself is a must - be main character. His growth as a ninja and his dream of becoming Hokage could be intertwined with the X - Men's mission of promoting mutant - human coexistence. And Rogue could also be a main character. Her power - absorbing ability would be very unique in the context of the Naruto world.
I think Naruto, Rogue, and Cyclops could be main characters. Rogue's power - absorbing ability could be an interesting element when combined with Naruto's chakra - based powers. And Cyclops could be the leader - like figure guiding their team - up against common enemies. The three of them could have a really complex relationship, with Rogue sometimes being a bit of a wildcard due to her power and Naruto and Cyclops trying to keep the team focused.
Hinata could be a main character as well. Her gentle yet strong - willed nature could bring a different dynamic to the story. She might be the one to initially bridge the gap between the Naruto characters and the Men in Black. And for the Men in Black side, Agent T could be a main character. He is known for his tech - savvy skills, and in the fanfiction, he could help the Naruto characters understand and utilize some of the advanced technology, while Hinata could teach him about chakra and ninja ways.
I think Rogue would be an interesting main character in a crossover. Her power - absorbing abilities could create some really unique situations, especially when she comes into contact with Clark or other powered individuals in Smallville. On the Smallville side, Lex Luthor could be a main character too. His devious nature and thirst for power could put him at odds with both the X - Men and Clark, making for a complex and engaging story.
Obviously Naruto would be one of the main characters. He could bring his unique ninja abilities and his indomitable spirit to the Titanfall universe. Another main character could be a Pilot, maybe a young and inexperienced one who Naruto befriends and helps grow. And a Titan itself could also be considered a main character in a way, as it has its own personality and capabilities that interact with Naruto and the Pilot.
In a Naruto x Shake It Up fanfiction, Naruto and Flynn could also be main characters. Flynn is always full of surprises and his comical nature along with Naruto's heroic and sometimes clueless nature about the modern world (since Shake It Up is a more modern - day setting) would create a lot of humorous and adventurous situations. Also, Gaara from Naruto could be brought in. His brooding personality would contrast well with the energetic Shake It Up characters.
Obviously, Naruto would be the central character. But in the genderbend version, characters like Sasuke, Sakura, Hinata, etc. would be genderbent. Sasuke as a female could bring a whole new dynamic to the story. She might be more of a femme fatale type, still having her strong will and desire for revenge but with a different charm. Sakura as a male could be the big - hearted but sometimes clumsy character, always trying to prove himself to Naruto. Hinata as a male could be more shy and reserved, yet still having a deep - seated love for Naruto.
Sasuke could also be a main character in such a fanfiction. His thirst for power and his Sharingan could make him a key figure. He might be interested in the advanced technology in Ghost in the Shell as a way to further his own goals. And perhaps he would cross paths with some of the Section 9 agents.
Well, Naruto is a must - have as the main character. In terms of the Jedi, Rey could be in the harem. Since she has a lot of potential and is learning about the Force, she would be interested in Naruto's abilities. Also, Padmé Amidala could be included. Even though she's not a Jedi, she has a strong presence and could be attracted to Naruto's heroic nature. And of course, there could be other original Jedi characters created specifically for this fanfiction.
Another option could be Naruto and Luna. Luna is all about music and Naruto is about ninjutsu. But they could bond over their passion for their respective crafts. They might find that they have a lot in common in terms of determination and drive. And together, they could face any challenges that come their way in this fanfiction world.
Mr. Sinister would be a great main villain. He's always had his own sinister plans for mutants. In a 'Termination' scenario, he could be taking advantage of the chaos to further his experiments on mutants, seeing it as an opportunity to create more powerful mutants under his control.