It could be Orochimaru. He's always interested in new forms of power. In this fanfic, he might discover the Monster Rancher world and try to use the monsters there for his evil experiments and plans. He could be trying to create some sort of ultimate monster by combining the powers of the Naruto universe and the Monster Rancher monsters.
Maybe a powerful and corrupt Monster Rancher could be the main antagonist. This person could be jealous of Naruto's natural ability to bond with monsters. So, they try to undermine Naruto at every turn, using their own powerful monsters to attack Naruto and his friends. They might also be involved in some sort of illegal monster trading or other unethical practices in the Monster Rancher world, which Naruto has to stop.
Obviously Naruto is one of the main characters. He's likely the central figure around which the story of the ranch and the monster girls revolves. His ninja skills and personality traits would play a big role in how he manages the ranch.
It could be Orochimaru. He has always been interested in experimenting with new forms and powers. If Naruto becomes a monster, Orochimaru might see him as a perfect specimen to study or use for his own evil plans.
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.