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 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.
Voldemort could be one of the main antagonists. He could follow the female Harry Potter through the portal to Middle - earth, causing chaos there. Also, the orcs and other dark creatures from Middle - earth like the Nazgûl could be antagonists. They would oppose the female Harry Potter and the hobbits or dwarves she teams up with.
Obviously, the fem Harry Potter would be one of the main characters. And perhaps she could meet Naruto in an anime world. Naruto's determination and her own magic skills would make them a great duo to face challenges together.
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.
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 someone new, a dark wizard who has learned about Naruto's reincarnation and wants to use his power for evil. This new villain might try to manipulate Naruto into using his chakra in a wrong way. Or perhaps it could be a combination of Voldemort and some of Naruto's old enemies from his previous life who somehow find a way to merge their powers in the Harry Potter world.
A possible main villain could be Voldemort who somehow gains knowledge of Naruto's world and uses it to his advantage. He could learn to use chakra and combine it with his dark magic. He might create some sort of hybrid minions that are part - Death Eater and part - ninja. This would make him even more powerful and a greater threat to both the wizarding world and Naruto's world.
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.
A powerful demon lord from the underworld could be the main villain. This demon lord could be seeking to expand his territory into the Naruto world, using his dark magic and hordes of minions.
Kaguya could be a great main villain for this. Imagine Kaguya emerging on Halloween night, her already otherworldly appearance made even more menacing with spooky Halloween - like enhancements. She could use the energy of the night to her advantage, trying to plunge the world into eternal darkness, and Naruto and his friends have to stop her.