Maybe it's a group of shinobi from a rival village. They see Naruto as a threat to their village's power and influence. With him in the Bingo Book, they think it's a legitimate chance to eliminate him and send a message to Konoha.
Maybe it's a powerful enemy from outside the village who has infiltrated the bingo book system. They see Naruto as a major threat to their plans and so secretly added him to the book, so they can send their minions to take him out without raising too much suspicion.
The plot might involve Naruto going undercover while being in the Bingo Book. He could be trying to find out who put a high price on his head and why. Along the way, he may encounter old friends who are conflicted about his situation in the Bingo Book.
Well, Naruto is surely one of the main characters as the title implies it's centered around him. His friends like Sasuke and Sakura are likely to also be important characters, as they are usually involved in Naruto's adventures.
The Organization in the Claymore world could be the main antagonist. They already have a lot of secrets and do some morally ambiguous things. If Naruto shows up and starts changing the status quo, like teaching Claymore warriors to be more independent, the Organization might see him as a threat and try to eliminate him.
It could be a rogue ninja who was once a student of Orochimaru and has now developed his own dangerous jutsu. He wants to take over the ninja world and believes the old ways are holding everyone back.
Orochimaru could be a great antagonist. He might want to use Shenron's power for his own dark experiments. He could try to steal the dragon balls and manipulate the wishes to gain immortality or create an army of powerful, immortal ninja.
It could be someone who opposes Naruto's newfound admiration for Ganondorf. Maybe a traditionalist ninja who thinks Naruto is straying from the true ninja path by getting influenced by Ganondorf.
Lex Luthor could be a great antagonist. He's always looking for power and knowledge. If he discovers Naruto's abilities, he might try to use them for his own gain or see Naruto as a threat to his plans in Smallville.
It could be Orochimaru. He's always been interested in unique powers and abilities. The idea of X - 23's mutant abilities and Naruto's jinchuriki powers would be very appealing to him. He might try to capture them both to use in his experiments to gain ultimate power.
A new character could be created as the antagonist. For example, an Uchiha who has been corrupted by the power of the Sharingan and wants to use Naruto's special Uchiha - related abilities for his own evil purposes. This character could be jealous of Naruto's unique position within the Uchiha - related story and try to take it from him.