In the Naruto world, it could be Orochimaru. He might be interested in Naruto's newfound Pokémon - related powers and try to capture him to experiment on him. Orochimaru is always after power, and Naruto's unique abilities could be very appealing to him.
Another possible antagonist could be a new, powerful dark Pokémon that is envious of Arceus's relationship with Naruto. This dark Pokémon could try to corrupt Naruto or turn him against Arceus in order to gain power over the Pokémon world and the Naruto world. It would be a formidable foe as it combines the dark powers of the Pokémon world with the knowledge of Naruto's world.
Maybe a group of dark - type Pokémon that have banded together and are trying to overthrow Arceus. They view Naruto as an easy target at first, but quickly realize he is a formidable opponent with his ninja skills and new Pokémon - related powers. They would constantly try to undermine Naruto and his efforts to protect the Pokémon world.
Another possibility is that some rogue ninja who have a vendetta against Hanzo might target Naruto as a way to get back at Hanzo. They could see Naruto as Hanzo's weakness and try to harm or kidnap him, which would then lead to a series of battles and confrontations in the fanfiction.
Well, it could be that Arceus, being a powerful and god - like Pokémon, sees Naruto's potential and decides to take him under his wing. Maybe Arceus helps Naruto gain new powers related to Pokémon abilities. For example, Naruto could learn to use Pokémon moves in his battles against the Akatsuki or other enemies in the Naruto world.
It could be other villages that see the alliance between the Raikage and Naruto as a threat. For example, some of the more power - hungry villages might fear that the combination of the Raikage's strength and Naruto's abilities would tip the balance of power in the ninja world. So, they would try to undermine their relationship or even attack them directly.
One possible main antagonist could be Frieza. Imagine if Frieza somehow found his way into the Naruto universe. He would be attracted to the chaos and power struggles there. Goku and Naruto would have to team up to stop him from taking over the Naruto world. Frieza's cold - blooded nature and his desire for power would put him at odds with our heroes. His powerful abilities would be a huge threat to both Naruto and Goku, especially since Naruto is still learning about the new powers Goku is teaching him.
The main antagonists could be the traditional enemies of Camelot like Morgana. She might see Merlin's act of adopting Mordred as a threat to her plans. Also, some of the knights or nobles in Camelot who are superstitious and believe Mordred is a danger just because of the prophecies could be antagonists. They might try to separate Merlin and Mordred or even harm Mordred.
Perhaps there are some anti - Uchiha elements within the village that are not happy with Naruto adopting Sarada. They could try to undermine her training or create problems for Naruto and Sarada. They might spread false rumors or try to isolate Sarada from the rest of the village.
Arceus, being a god - like being, would probably be very calm and wise. However, in this fanfiction, as it has a relationship with Naruto, it might also show a more affectionate and protective side. It could be a bit aloof at times due to its divine nature, but still show deep care for Naruto.
The Death Eaters could still be the main antagonists. They might see Fenrir's new alliance with Harry as a threat. Since they once used Fenrir for their dark deeds, they don't want him to turn good and expose their secrets.
It could be a group of rogue ninjas from the new time period who see Jiraiya as a threat to their plans. Since he has different skills and knowledge, they might want to eliminate him.