Maybe there are some bounty hunters. They've heard about the valuable Bioraptor Riddick and are after him for the reward. They don't care that Harry has adopted him and will stop at nothing to get Riddick. They could be really tough and experienced, making it a great challenge for Harry to protect Riddick from them.
There could be a powerful and cruel dictator in the world of the fanfiction. He sees the Bioraptor Riddick as a weapon or a symbol of power. When he learns that Harry has adopted Riddick, he sends his troops to capture Riddick. This dictator is used to getting what he wants and won't let Harry or Riddick's new - found bond stand in his way.
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.
The story could start with Harry coming across a young and lost Bioraptor Riddick. Harry, out of compassion, takes him under his wing. Riddick, at first, might be wild and unruly, but Harry's patience and kindness gradually tame him. They could live in a world where there are other threats, like evil hunters or a corrupt government that wants to use Riddick for their own purposes. Harry and Riddick then have to work together to outwit their enemies, with their relationship growing stronger through each trial.
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.
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.
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.
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.
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 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.
It could be Sally's ex - partner if there was a not - so - nice one. This person might want to take the daughter back out of spite or some wrong idea that Percy isn't a good enough caretaker.
One possible antagonist could be Sabretooth. He might see Wolverine's newfound fatherly relationship with Peter as a weakness and try to use Peter to get to Wolverine. Sabretooth could be jealous of the bond Wolverine is forming and want to destroy it.