It could be a rogue ninja who has mastered the devil breakers in a very dark way. He might use them to gain power and control over the ninja world, seeing Naruto as the main obstacle to his plans.
There could be a secret organization that has been developing super - powerful devil breakers in secret. Their leader believes that the ninja world needs to be 'cleansed' and wants to use these advanced devil breakers to do so. Naruto stands in their way as he believes in the co - existence of different powers and ways of life in the ninja world. So, this organization's leader becomes the main antagonist as Naruto tries to stop their genocidal plans.
In this kind of fanfic, it might be that a group of rogue ninjas obtain devil breakers and start causing chaos in the ninja world. Naruto, being the hero he is, decides to study these devil breakers to find their weaknesses. He meets an old hermit who has some knowledge about them. Along the way, Naruto also has to deal with his friends' doubts about using such foreign and potentially dangerous technology. He has to prove that he can use it for good and stop the rogues before they destroy everything he holds dear.
It could be a powerful devil who sees Naruto as a threat to his rule in the devil realm. Maybe this devil wants to use Naruto's power for his own evil purposes and Naruto has to resist.
It could be a powerful devil who has the ability to control minds. This devil could manipulate some of Naruto's friends and turn them against him, creating a lot of internal conflict within Konoha.
Another option could be a group of rogue robots who have their own set of rules and don't like the idea of Bender and the Robot Devil being so prominent. They could band together to try and take over the areas that Bender and the Robot Devil operate in. They might be more brutal and less interested in the games and deals that the Robot Devil usually plays, making them a very different kind of antagonist compared to the Robot Devil.
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.