There could be a rival kingdom led by a tyrant king. This king sees Naruto's village as a valuable asset and wants to conquer it. He has a large army of knights and foot soldiers. His knights are well - trained and equipped, and he uses underhanded tactics to try and defeat Naruto and his comrades in battle.
Maybe the Akatsuki as a whole. They are a group of powerful and dangerous ninjas. The Black Knight's presence might disrupt their plans to collect all the tailed beasts. They would see him as an obstacle and try to eliminate him. For example, Pain might think the Black Knight is a threat to his vision of peace through pain and send his subordinates to fight him.
It could be Orochimaru. In the medieval knight setting, he might be a dark sorcerer who wants to use the power of the knights for his own evil purposes. He could be trying to steal the holy relics of the kingdom which are said to grant great power, and Naruto, as a knight or someone with knight - like qualities, has to stop him.
A new character could be created as the main antagonist. For example, a powerful sorcerer from a far - off land who has come to Hyrule seeking its magical energy. He wants to use the power of the Dragon Knight to open a portal to a realm full of dark magic.
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.