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.
A devil queen or king. They could be from a far - off dimension and see the world of Naruto as a new territory to conquer. They send their minions to wreak havoc in Konoha and Naruto has to step up as a devil hunter to stop their invasion. This antagonist would be extremely powerful and have a whole army of devils at their command, making it a huge challenge for Naruto and his friends.
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 rogue hunter nin who doesn't like the idea of Naruto, an outsider, joining their ranks. This rogue hunter nin might see Naruto as a threat to their power and influence within the group.
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.
It could be a powerful demon lord who wants to conquer both the Naruto universe and the Devil May Cry world. This demon lord might have the ability to manipulate chakra and also use demonic powers, making it a formidable foe for both Naruto and Dante.
It could be a rogue hunter who has his own twisted ideas about the use of Nen. This hunter might see Pokkle and Ponzu as obstacles in his quest for power and knowledge. He could try to capture them to steal their Nen abilities or the information they have about certain areas of the Hunter x Hunter world.
It could be an evil poacher who wants to capture all the dalmatians for their fur. He would be a formidable antagonist for the hunter as he has his own set of cruel hunting skills.
It could be someone from the Naruto universe who doesn't like Naruto's newfound fascination with Aku. For example, Danzo might see Naruto's interest in Aku as a threat to the stability of the village and try to stop Naruto from further exploring Aku - related things. So, Danzo could be the main antagonist in this case.
There could be a group of poachers who are not just after regular game but are also involved in some dark magic. They oppose the hunters and especially Percy when he tries to stop their illegal and dangerous activities. They might have powerful backers or magic items that make them a formidable foe for Percy and the other hunters.
There could also be a corrupt official within the Hunter's Guild. This person doesn't like the way the Handler and Hunter are operating, perhaps because they are too independent or they are getting in the way of some underhanded scheme the official has. So, this official uses their power to try and undermine the duo, from withholding resources to sending them on extremely dangerous and near - impossible missions.
One idea could be Naruto discovers a hidden realm where devil hunters operate and he has to learn their ways to save his village from a devil invasion.