The main antagonist might be an organization that wants to use the gunblade to take over the shinobi world. They see Naruto as a threat because he has the weapon and they will stop at nothing to get it from him. They send their best assassins and fighters to face Naruto in battle, constantly putting him and his village in danger.
It could be a powerful rogue ninja who has a vendetta against Naruto specifically because of the gunblade. Maybe he was once part of a group that was tasked with protecting the gunblade, but it was lost under his watch, and he blames Naruto for having it now.
Perhaps a dark and ancient spirit that was sealed away long ago is awakened by the presence of the gunblade in Naruto's hands. This spirit wants to use the gunblade to break free from its remaining seals and bring chaos to the world. It possesses the bodies of strong shinobi to fight Naruto, making it a very difficult enemy to defeat as Naruto has to not only fight physically but also find a way to exorcise the spirit from its hosts.
One possible plot could be that Naruto discovers the gunblade in a hidden, ancient shinobi arsenal. He initially struggles to master it as it combines two very different combat elements - ranged shooting and melee slashing. However, with his determination, he gradually learns to use it effectively in battles against new, powerful enemies that are immune to his regular jutsu.
It could be a rogue ninja from a forgotten clan who is jealous of Naruto's new - found power from his hidden bloodline. This antagonist might try to steal Naruto's bloodline ability for himself.
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.