Maybe an Asgardian traitor who has been exiled and found his way into the Inuyasha world. This villain would want to use the chaos in the Inuyasha world and the power of the Shikon Jewel shards to create an army and then return to Asgard to take revenge. He would be a threat because he knows Asgardian magic and combat techniques, and he could also manipulate the demons in the Inuyasha world to do his bidding.
A being from a third realm that has been observing both Asgard and the Inuyasha world. This entity sees the potential power that could be gained from combining the magic of the Shikon Jewel and the power of Thor's hammer. It enters the Inuyasha world and starts causing destruction and chaos in order to draw out Thor and Inuyasha. Once they are both in its clutches, it plans to steal their powers and become an all - powerful being.
It could be a powerful demon from the Inuyasha universe who has somehow managed to gain the ability to absorb the power of gods. This demon would see Thor as a prime target to drain his powers and use them to conquer both the Inuyasha world and potentially other realms. The demon's dark magic and newfound god - like powers would make it a formidable foe for Thor and Inuyasha's combined forces.
A powerful dementor - like being that has been corrupted by Asgardian dark magic. This entity could be draining the life force of both wizards and Asgardians. It would be up to Thor and Harry Potter to find a way to stop it, as it poses a threat to both of their worlds.
It could be an evil ninja who has learned to use dark magic and wants to take over Pixie Hollow for its magic. He sees the fairies' magic as a source of power to enhance his own dark jutsu.
Another option could be Kabuto. He has been influenced by Orochimaru and is always looking for ways to gain more power. He might target Kurenai to learn more about her genjutsu and Naruto because of his status as a hero. Kabuto could be plotting to use their powers to further his own goals in the ninja world.
Perhaps it could be a character who is jealous of both Naruto and Hercules. A sorcerer who was once shunned in both worlds and now wants to prove himself by defeating them. He could use dark magic to create chaos and try to stop Naruto and Hercules from uniting and using their combined powers.
It could be Bowser who has somehow gained the power of a powerful ninja jutsu. He uses this new - found power to take over both the Mushroom Kingdom and start invading the Naruto world. His fire - breathing ability combined with ninja techniques would make him a formidable foe for Naruto and Mario.
Hush could be an interesting choice. He could be spreading false rumors and causing distrust between the heroes and the citizens of both cities. His knowledge of Gotham's underworld and his ability to manipulate people could make him a formidable foe for Batwoman and Arrow. They would need to uncover his true identity and stop him before he completely destroys the relationship between the two cities.
It could be Orochimaru. Imagine he discovers the power of the ocean in Moana's world and wants to use it for his own dark experiments. He could start corrupting the sea creatures and causing chaos on Moana's island. Naruto, having faced Orochimaru before, would know his weaknesses and team up with Moana to stop him.
Vilgax could be a great main villain. He has a long - standing rivalry with Ben and his presence would add a lot of tension. He could see Albedo as a useful tool or a threat depending on the situation. Another option could be an original villain created specifically for the crossover. Maybe a powerful alien entity that wants to use Albedo's knowledge and Ben's powers for its own evil purposes. A third choice could be Aggregor, who might be after some new power source that is related to both Albedo and Ben.
The Reverse Flash could also be a main villain in this crossover. He travels to the Smallville universe to cause trouble. He might target Clark, thinking that by eliminating him early, he can change the future in his favor. This would force Barry and Clark to work together to stop the Reverse Flash's evil plans.
One possible plot could be that Thor somehow gets transported to the Inuyasha universe. Thor's powerful hammer and lightning powers would be a huge asset or a source of conflict. Maybe the demons in the Inuyasha world see Thor as a threat or a powerful ally to be manipulated. Inuyasha and his group might initially be wary of Thor but then realize they can work together to defeat a common enemy, like a powerful demon that is causing chaos across the land.