It could be a corrupted version of the Cheshire Cat. Maybe it has been influenced by dark magic and now uses its ability to disappear and reappear to mislead Harry and lead him into dangerous situations. Harry would have to figure out how to overcome this devious foe.
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.
The Queen of Hearts would make a great main villain. Her tyrannical rule and quick temper in the original Wonderland story could be amplified in a fanfiction. She could be a powerful dark magic user who sees Harry as a threat to her rule and tries to stop him from achieving his goals in Wonderland.
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.
Perhaps the main villain is actually a corrupted version of a well - known character. For example, if Hermione was somehow influenced by the dark magic associated with the runestone path and turned against Harry. It would be a very unexpected and heart - wrenching twist, as she has always been such a loyal friend. But the power of the runestone path could be so strong that it changes her fundamental nature.
Maybe a new character, a Muggle - born wizard who was shunned by both the Muggle and wizarding worlds. This character, out of bitterness, decides to combine Muggle technology and magic to create the droid army and rule over both worlds. He would see Harry Potter and his friends as the main obstacles to his grand plan.
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.
Perhaps an old Hufflepuff alumni who has turned to the dark side. This person was once a great student but became corrupted over time. They return to Hogwarts with the intention of using the Hufflepuff house as a base for their dark plans. They manipulate the Hufflepuff students, taking advantage of their kindness and hard - working nature, and turn it into a means to an end for their evil deeds. Harry gets caught up in this as he tries to figure out who this mysterious villain is and stop their plans.
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 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.
Maybe the main villain could be a corrupted Hogwarts professor. This professor could be secretly teaching dark magic to students and when Harry's child discovers this, they become the target. The professor wants to stop the child from revealing their dark secrets and will go to great lengths to do so, making them a formidable villain in the fanfiction.
A possible main villain could be an ancient sorcerer from the new dimension who has been awakened from a long slumber. He's enraged that the wizarding world has been interfering with his dimension's magic, and decides to take revenge on Harry Potter's world. He has powers that are unknown to the normal wizarding world, like the ability to control time in his dimension, which makes him a formidable foe.