Perhaps some of the more mysterious characters from the series could take the lead. For example, Isabel Kabra. Her devious nature could add a whole new layer of intrigue to the crossover fanfiction. She could be working with or against the other characters in unexpected ways, creating a lot of tension and interesting plot twists.
Definitely Naruto himself. He's the main character of the Naruto series, so he has to be there. In a crossover with Attack on Titan, he could meet Eren. Naruto's determination and Eren's drive to protect his people could make for an interesting dynamic between them.
A group of scientists who were involved in creating the Indoraptor in the first place could be main characters. They might have to face the consequences of their creation when it crosses over into another world or situation. They would be trying to either control it or destroy it.
If it's a crossover with the DC universe, Batman could be the main character. He would use his detective skills and arsenal of gadgets to face the Deathclaw. His dark and brooding nature would make for an interesting contrast against the brute force of the Deathclaw.
Godzilla himself would obviously be a main character. His actions and reactions would drive much of the story. Another possible main character could be Pinkie Pie. Her unique view of the world and her ability to make friends with anyone could play a role in how the ponies deal with Godzilla. Maybe she throws a party for Godzilla to make him feel welcome.
If it's a crossover with Final Fantasy, Cloud Strife could be a main character. He could bring his sword - fighting skills to the Mario Party world. His serious and brooding personality would contrast with the more light - hearted Mario characters, creating some interesting interactions during the story and mini - games.
If it's a crossover with the Harry Potter universe, Hagrid could be a main character. Hagrid loves all kinds of strange and dangerous creatures. He might see the Indominus Rex as a misunderstood beast and try to tame it, but quickly realize that this dinosaur is far more dangerous than any creature he's dealt with in the wizarding world.
Definitely Naruto would be a main character. He is the protagonist of the original series and would be the one to drive the story forward in the crossover. Then, perhaps a new character could be introduced who has a special connection to the bone - related aspect. This character could be from another world or a long - lost clan in the Naruto universe. Also, Gaara could be a main character. His sand powers could interact in interesting ways with the bone - related elements, like his sand protecting him from bone attacks or being able to incorporate bones into his sand defenses.
Definitely, Cortana could be a main character in a 'halo anime crossover fanfiction'. If she were in the world of Code Geass, she could help Lelouch with his strategic plans, using her vast knowledge and intelligence. Another option is the Elites from Halo. They could be the main characters in a crossover with My Hero Academia. Their physical strength and warrior culture could be contrasted with the superheroes in that anime, and they could have some interesting interactions with the students at UA High.
Obviously, Naruto would be one of the main characters. He's the protagonist of the Naruto series and would be the main link to the ninja world in this crossover. Another could be a young Kitsune, maybe one that's just coming of age in the Kitsune world. Their paths cross, and they have to learn to work together.
If the 'accel world crossover fanfiction' is with a high - tech world, Ash Roller could be a main character. His unique style and skills in the 'accel world' would translate well in a high - tech crossover. He could be the one to introduce the 'accel world' concepts to the new world. And if it's a crossover with a more mysterious world, Sky Raker could be a main character with her wisdom and mysterious past.