Another option is a powerful dark wizard from the past in the wizarding world who has been banished to the underworld. He wants revenge on the wizarding world and plans to use Hades' power to break free and wreak havoc. Harry Potter must then face this resurrected dark wizard and prevent him from using the underworld as a base for his revenge.
The main antagonist could be a dark wizard who has mastered water - based magic and has made a pact with a powerful sea monster. This dark wizard wants to rule both the wizarding world and the underwater world. He sees Harry Potter as a threat to his plans in the wizarding world and Aquaman as a hindrance in the underwater realm.
Voldemort could easily be the main antagonist. His goal of taking over the wizarding world and his use of dark magic would put him in direct conflict with Boromir and Harry. Boromir's sense of justice would not allow Voldemort's tyranny to stand, and Harry has his own vendetta against the Dark Lord.
Maybe a rogue wizard who has found a way to access the technology from Kara's world and wants to use it to rule both the wizarding world and any other world he can reach. He would be opposed by both Harry Potter, who wants to protect his world, and Kara Thrace, who doesn't want her technology misused. This wizard could combine dark magic with advanced technology to create powerful and dangerous weapons and spells.
In this type of fanfiction, Voldemort could still be the main antagonist. But the way Harry approaches him would be very different. With Riddick's influence, Harry might see Voldemort as just another powerful enemy to be taken down in a more direct, perhaps violent way, rather than through the more magical and somewhat convoluted ways in the original series.
It could be Voldemort and Loki. Voldemort, being the main villain in the Harry Potter series, is power - hungry and wants to rule the wizarding world. Loki, from the God of Thunder universe, is known for his trickery and his own desires for power. They could team up, thinking that they can use each other to achieve their goals. Voldemort could be interested in Loki's ability to deceive and Loki could see the potential in Voldemort's dark magic. They would be a formidable pair against Harry Potter and Thor.
It could be a dark fairy who wants to use the power of both the wizarding world and Pixie Hollow for her own evil purposes. She might try to steal the magic from Hogwarts and the pixie dust from Pixie Hollow to become all - powerful.
Maybe a powerful and ancient being that has been awakened by the mixing of the two magical worlds of Harry Potter and Twilight. This being is enraged by the existence of both wizards and vampires and wants to wipe them out. Harry and Rosalie, being representatives of their respective groups, must join forces to stop this ancient and powerful foe. Their combined skills and the unique powers of their friends from both worlds would be crucial in this fight.
Maybe the main antagonist could be Ra's al Ghul. He's always interested in power, and if he got his hands on some magic from the Harry Potter universe, he could become an even greater threat. He could try to use the magic to bring about his vision of a 'perfect' world, which would be at odds with both Harry's and Nightwing's ideas of justice. So they'd have to join forces to stop him from achieving his goals.
It could still be Voldemort. Even with Revan's training, Voldemort's power and his army of Death Eaters would pose a significant threat. Harry would have to use his newly acquired skills from Revan to finally defeat Voldemort once and for all.
Perhaps a dark wizard from the Harry Potter universe who has heard about the Cullens' unique vampire abilities and wants to harness that power for himself. He could be a follower of Voldemort who escaped the final battle and is now looking for new ways to gain power. So he targets the Cullens, thinking their powers can help him rule both the wizarding and vampire worlds, and Harry has to stop him.