It could be a rogue ninja from Naruto's world who has some sort of vendetta against Naruto and sees Rachel Stanley as an easy target to get to Naruto. This ninja might have some dark jutsu that he uses to try and stop them from achieving their goals.
The fanfic could also revolve around Rachel Stanley somehow getting transported to the Naruto universe. She might be a bit lost at first, but Naruto takes her under his wing. They could then embark on a journey to find a way to send Rachel back home, all while Naruto teaches her about chakra and ninja skills. Along the way, they form a deep friendship that changes both of them.
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.
It could be a rogue ninja who has mastered parkour to an extreme level. He uses his skills to steal important ninja artifacts and Naruto has to stop him. This antagonist would be very fast and agile, making it difficult for Naruto to catch him using normal ninja techniques.
Madara could still be the main antagonist even in a 'naruto bankai fanfic'. He senses Naruto's new power and realizes it could be a threat to his plans of world domination. He adapts his strategies and attacks Naruto with all his might, trying to prevent Naruto from fully mastering and using his Bankai - inspired power to its fullest potential.