It could be a character who is jealous of Naruto's new dragon powers. Maybe someone who has always been in competition with Naruto and now feels even more threatened by his enhanced abilities.
Perhaps an ancient evil that has a vendetta against the eastern dragons. Since Naruto is now associated with them, this evil force sees him as a target. This antagonist could be trying to disrupt the balance that Naruto, as a dragon - like figure, is supposed to maintain. They might use dark magic or forbidden jutsu to try and defeat Naruto and spread chaos in the ninja world.
Another possibility is a group of rogue ninjas who see Naruto's transformation into a dragon - like being as a threat to their own power - hungry plans. They might team up to try and take Naruto down, thinking that by eliminating him, they can gain more control over the ninja world and its resources.
The World Government could be the main antagonist in a more complex way. They could be secretly manipulating events to pit Dragon and Luffy against each other. For example, they could spread false rumors about Luffy being a tool of the revolutionaries, which would make other pirate crews and kingdoms target him, and at the same time make Dragon look bad for having a son who is causing so much chaos. This would force Dragon and Luffy to either fight each other or find a way to clear their names together.
Another possibility is a corrupted dragon spirit that has been awakened due to the mixing of the two worlds. This spirit could be spreading chaos and trying to destroy both the ninja world and the dragon world. Naruto would have to figure out a way to stop it, as it has powers that are beyond what he has faced before.
It could be a powerful dragon hunter. This person would see Naruto's dragon as a prize to be captured or killed. They might have a personal vendetta against dragon riders in general.
There could be a powerful sorcerer who is jealous of the unique bond between Naruto and the dragon maids. This sorcerer wants to break that bond and take control of the dragon maids' power for himself. He uses dark magic to create illusions and obstacles for Naruto and the dragon maids, trying to turn them against each other so he can achieve his evil goals.
There could be a group of dark ninjas who see Naruto's connection with the dragon as a threat. They believe that Naruto and the dragon together could become too powerful and disrupt their evil plans. So, they set out to destroy the dragon and capture Naruto to prevent them from achieving their goals.
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.