Maybe a powerful and ambitious wizard from a foreign magical land. He sees the post - Voldemort wizarding world in Britain as weak and ripe for the taking. He wants to impose his own version of a new order, which is really just a dictatorship in disguise. He uses his unique foreign magic to create chaos and gain power.
It could be a rogue Death Eater who escaped punishment and has been biding his time. He might have a new, more insidious plan to bring back the dark ways of Voldemort.
It could be a long - lost relative of Voldemort, carrying on his dark legacy.
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.
It could be a rogue member of the Order. Maybe someone who has their own agenda and decides that Harry is a threat to their plans. So they manipulate the Order into kidnapping Harry, but then they have their own evil intentions for him.
It could be a powerful veela who has a grudge against Hogwarts. Maybe a Hogwarts student in the past wronged her family. She uses her charm and powerful magic to try and bring chaos to the school. She first lures some of the male students with her beauty and then uses them to carry out her devious plans. For example, she might make them steal important magical artifacts from the school that are used to keep Hogwarts safe.
There is a possibility that an ancient and powerful dark creature could be the main villain. This creature, long forgotten in the wizarding world, resurfaces and targets Harry's son. It might believe that the boy has some special power or is the key to something it desires. As a result, it lures the son away and hides him in a remote and dangerous place. Harry has to figure out what this creature is and how to defeat it to get his son back.
The Slaughterhouse Nine could be the main villains. Their sadistic and unpredictable nature would pose a huge threat to Harry. Each member has their own unique and terrifying power. Harry would have to rely on his magical knowledge and any allies he can make in Brockton Bay to survive and stop the Nine from causing more chaos in the city.
It could be a descendant of Voldemort. Even though Voldemort was defeated in the original series, his ideas might have been passed down through generations. This new villain could be even more cunning and powerful, and they see Harry Potter, who has been frozen and is now back, as a threat to their plans of total wizarding world domination.
It could be a rogue wizard who was once a student at Hogwarts and has a vendetta against the school. He was expelled for practicing dark magic and now he's back to cause trouble. Maybe he wants to steal some powerful magical artifacts from the school's vaults.
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 alternate version of Dumbledore. Maybe in this dimension, he was corrupted by power. He uses his vast knowledge and influence to control the wizarding world for his own ends. He manipulates the students at Hogwarts and uses dark magic in secret while maintaining a public facade of being a great wizard.