Another possible main antagonist could be Two - Face. His sense of justice, albeit a twisted one, would likely be at odds with Harry's more magical and morally - grey - area - free way of doing things. He might see Harry's use of magic as an unfair advantage and try to bring him down, especially if Harry's actions start to influence the criminal underworld that Two - Face is a part of.
Well, perhaps Harry Potter arrives in Gotham City and is appalled by the state of it. He decides to adopt some of the children who are in difficult situations. As he does this, he uses his Hogwarts education and magical skills to protect them from the likes of the Penguin and other villains. He might even introduce some magic into Gotham's society in a very subtle way, like using spells to improve the living conditions in the slums where he and the adopted kids live.
Scarecrow could also be a main antagonist. His fear - inducing toxins could be a real problem for Harry. Harry would have to use his magic to counter the effects of the fear toxin and also figure out a way to stop Scarecrow from spreading it all over Gotham.
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.
Voldemort would still be a major antagonist. His goal of ruling the wizarding world and eliminating Harry Potter would remain. However, there could be new antagonists added due to Hawkgirl's presence. For example, some Thanagarian villains might follow Hawkgirl to the wizarding world and see the chaos Voldemort is causing as an opportunity to gain power for themselves. They could try to form an alliance with Voldemort or simply try to take over the wizarding world on their own.
It could be a group of scientists who created the Bioraptor Riddick for some evil purposes. When they find out that Harry has adopted Riddick, they want to take him back to continue their experiments.
Some pure - blood supremacist wizards might oppose Harry. They may not like the idea of a half - blood like Harry having so much control over a city and could try to create unrest. Also, there could be some non - magical criminals who target the city because of its new magical elements under Harry's leadership.
One main antagonist could be Scarecrow. His fear - inducing tactics could be used against Marinette and the people she's trying to help. He might see her as a threat to his plans of spreading fear throughout Gotham. Also, Black Mask could be an antagonist. He would likely oppose Marinette if she tries to clean up the criminal underworld in Gotham, as it would cut into his business and power.
In this fanfiction, Voldemort or his remaining followers could be major antagonists. They wouldn't like the idea of Harry having new allies in Percy and the demigod community. From the Percy Jackson side, the Titans or some of the more malevolent gods might not be happy with the alliance either. They could try to break it up or cause trouble for the two boys, seeing them as a potential force against their own plans.
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 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.