It could be a rogue ninja who has a vendetta against Naruto and sees Hinata as a way to get to him. This antagonist might try to disrupt the relationship between Naruto and Hinata where Hinata wants Naruto to be dominant, for example by spreading false rumors about Naruto's methods of training Hinata.
A new threat from outside the village, like a powerful group of bandits. They see Hinata as a vulnerable target because she's relying on Naruto to be dominant. They try to break her spirit by attacking her when she's on her own during a time when Naruto is away on another task, which Naruto then has to come back and deal with, reasserting his dominance in protecting Hinata.
Maybe an old - fashioned ninja in the village who doesn't believe in Naruto's unorthodox ways. He could be the antagonist as he tries to stop Naruto from being dominant over Hinata in her training or in any situation. He might think Naruto is being too reckless and not following the traditional ninja code, and this causes conflict with Hinata who trusts Naruto's methods.
One possible plot idea could be that Hinata is in a training scenario where she wants Naruto to be really strict and dominant in teaching her new jutsu. For example, Naruto could push her to her limits in a sparring session, making her improve rapidly.
There's a possibility that the main antagonist is an internal force within Naruto himself. His desire to be alone could be a manifestation of some dark part of his psyche. This 'inner antagonist' could be trying to make Naruto cut himself off from his loved ones completely, leading him down a path of self - destruction. And Naruto has to fight this internal battle while also dealing with any external threats that come his way during his isolation.
It could be a rogue ninja. This ninja might have a vendetta against the village that Sakura, Ino, Hinata are from. Yuri could be a target because she has some special ability that the rogue ninja wants to steal. The rogue ninja uses his dark jutsu to try and defeat the girls one by one, but they use their combined skills and friendship to fight back.
It could be an old rival from Percy's past, someone who has always been jealous of Percy's abilities and has finally found a way to cause him great harm. This person would be a perfect antagonist as Percy would have a strong motivation to get revenge on them.
It could be other powerful ninja clans who see the fem Kyuubi's possessive behavior towards Naruto as a threat to their own power and influence. They might try to separate them.
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.