Maybe a powerful demon that was sealed on Skull Island long ago. With Naruto's arrival, the seal weakens and the demon starts to break free. It wants to take over the ninja world and sees Naruto as a threat. It uses the strange powers of the island to create obstacles for Naruto and his allies.
It could be a rogue ninja who has made Skull Island his base. He has found a way to control some of the dangerous creatures on the island and uses them to attack anyone who comes near. His goal is to find a powerful artifact on the island that he believes will make him invincible.
Obviously, the Red Skull himself could be the main antagonist. His evil nature and powerful abilities would make him a formidable foe for Naruto and his friends. He could use his knowledge of dark magic or advanced technology (if that aspect is brought into the fanfiction) to create chaos in the ninja world.
It could be a powerful rogue ninja who has made Zacks Island his lair. He might be hoarding some valuable resources on the island and sees Naruto as a threat to his plans.
One idea could be that Naruto is sent to Skull Island on a mission. He discovers unique chakra - based creatures there. He has to use his ninja skills and Sage Mode to survive and understand the mysteries of the island. Maybe he forms an alliance with some of the native beasts against a common enemy.
A powerful sorcerer who also wants to claim the island for his own could be the main antagonist. He sees Percy as an obstacle to his plans and tries to eliminate him. The sorcerer might have control over some of the dangerous creatures on the island and use them to attack Percy.
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.
Maybe a new character could be introduced as the main antagonist. This character could be from a hidden village that has been secretly observing Naruto's growth. They realize his potential as a weapon and plan to steal his power or use him to start a war against other villages.
Krampus himself could be the main antagonist. Since he is a figure known for punishing the naughty, his actions in the Naruto world might be seen as unjust. He could be going after ninjas without really understanding their motives, causing a lot of trouble for the main characters.
It could be a rogue ninja who also has somehow acquired bankai - like powers. This antagonist might be jealous of Naruto's newfound abilities and wants to prove that he is the stronger one. So he starts causing chaos in the ninja world, challenging Naruto at every turn.
It could be a rogue ninja who wants to disrupt Naruto's business to gain power. Maybe he's jealous of Naruto's success and popularity in the business world. He could try to steal Naruto's business secrets or sabotage his operations.
It could be a rogue Kumo ninja who is jealous of Naruto's power and wants to prove himself by defeating Naruto. This ninja might have some dark secrets and a grudge against Kumo as well.