Morgana could be a main antagonist. She has her own desires for power and may see Merlin's rise to kingship as a threat to her plans. So she tries to stop him at every turn, using her dark magic against him.
The lords who oppose magic in the kingdom could be antagonists. They don't trust Merlin because of his magic and will do everything they can to prevent a magic - user like him from becoming king. They might plot to frame him or undermine his reputation among the people.
A powerful sorcerer from a foreign land could be the antagonist. This sorcerer wants to take over the kingdom and sees Merlin as an obstacle. He tries to defeat Merlin in magical battles and also tries to turn the people against Merlin by causing disasters and blaming them on Merlin's magic.
There could be a new dark sorcerer who emerges. This person might be jealous of Merlin's position as king and a powerful sorcerer. They would try to bring chaos to the kingdom and usurp Merlin. Also, the neighboring kingdoms that are envious of Merlin's prosperous kingdom could send spies or even start wars, acting as antagonists.
In this fanfiction, the Church or religious authorities in Camelot could be the main antagonists. Vampires are often associated with the devil or evil in religious beliefs. So, they might see Merlin's transformation into a vampire as a sign of him being corrupted by dark forces. They would try to exorcise or destroy him, not understanding that he's still the same Merlin at heart, just with a different form and new powers.
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.
There could be an old dragon that has been in exile for a long time. This dragon might see Hiccup as a threat to its plan of taking over the dragon kingdom. So it tries to stop Hiccup from fully becoming a dragon or tries to use his new form for its own evil purposes.
Perhaps the very magic that made Harry a god has a sort of negative side - effect. This could manifest as a shadowy entity within Harry that tries to take over his mind and use his powers for evil. So, in a way, this internal struggle could be the main antagonist in the story.
One potential main antagonist could be a powerful pirate captain who sees Harry as a threat to his control over the seas. Maybe this captain has some dark magic powers as well.
The Hidden Leaf Village elders could be antagonists. If Naruto turns dark, they might see him as a threat to their power and try to stop him. Their actions against Naruto could further fuel his descent into darkness.
The Titans could be the main antagonists. They might oppose Percy's ascension to Olympian status because they see it as a threat to their own plans of overthrowing the Olympians.
Some jealous students at Hogwarts could also act as antagonists. They might be envious of Harry's newfound allure and use underhanded tactics to try and make his life difficult.
The Hidden Leaf Village itself could become the main antagonist. Since Naruto turns evil, the village that once nurtured him would now be against him. The village elders and some of the ninja who oppose Naruto's new evil ways would be in conflict with him. For example, Kakashi might be forced to fight against Naruto to protect the village.