Voldemort could still be the main villain in a different way. Suppose he discovers Tonks' unique connection to Harry and tries to use her as a weapon against him. He could manipulate her mind or put her in dangerous situations to force Harry to make sacrifices or bad decisions.
It could be a Death Eater who has somehow made a pact with a powerful force from Scorpian's world. This villain would be extremely dangerous as they'd combine the dark magic of the Harry Potter universe with the unknown and potentially deadly powers from Scorpian's realm.
It could be a new character that is a combination of a dark wizard and a Hollow. This creature would be able to use both dark magic and Hollow abilities. It would target both Hogwarts students and Soul Reapers. Ichigo and Harry would have to figure out its weaknesses, which would be a difficult task as it has powers from two very different universes.
Another option could be a new character created specifically for this crossover. This character could be a wizard who has studied the ninja arts and has become corrupted by power. He could start by causing chaos in the wizarding world, using his magic to mimic some of the more dangerous ninja techniques. Then, he could set his sights on the ninja world, seeing it as another source of power to be conquered. Fem Naruto and Harry Potter would have to put aside their differences and work together to stop him.
It could be a wizard who has gone mad with power and wants to control both the wizarding world and the underwater realm. He discovers a way to use dark magic to manipulate sea creatures and cause destruction in Aquaman's kingdom. He then sets his sights on Hogwarts as well, seeing it as another source of power.
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.
Lex Luthor from Supergirl's world could be the villain. He could somehow find a way to travel to the wizarding world and team up with some dark wizards. He wants to use magic to enhance his power and take over both worlds. Supergirl and Harry Potter would have to stop his evil plans.
It could be a new character created by the fanfiction author. Maybe a powerful wizard who was once shunned by the wizarding community and now wants revenge by stealing magic.
A dark wizard who has merged the dark arts with Wonderland's magic could be the main villain. He might have created some sort of dark Wonderland where all the creatures are under his control, and Harry has to break this control to restore balance.
It could be Orochimaru. He might be interested in Tenten's unique weapon skills and Naruto's power of the Nine - Tails. He could try to capture them to conduct experiments on how to combine their powers for his own gain. He might create some sort of hybrid - clone with Tenten's weapon - using abilities and Naruto's chakra.
A possible main villain could be a dark wizard who has learned some of the criminal tactics from the Detective Conan world. He could be using both magic and devious non - magical schemes to cause chaos. For instance, he might use spells to steal valuable items and then use the underworld connections in Conan's world to sell them.