Harry Potter himself could be the main character. Given his experience with fighting dark forces in his own world, he could be a natural fit to take on the role of a Sith hunter. He already has the courage and magical abilities.
Perhaps a new character could be the main character. A young wizard or witch who discovers a connection between the Sith and some dark magic in the Harry Potter world. This character could then embark on a journey to become a Sith hunter, learning about both universes along the way.
A new character could be introduced as a Sith Lord. Maybe a wizard who has been studying dark and forbidden magic from other dimensions. He could have a red lightsaber - like wand and use powers that combine magic and Sith - like abilities. For example, he could use mind control not just on muggles but also on some weak - willed wizards.
Perhaps a witch who has lost her family to witch hunters decides to take matters into her own hands. She disguises herself as a Muggle and tries to infiltrate the witch hunter's group to take revenge. This would make her a very interesting and complex main character.
A new student at Hogwarts, who has a mysterious past related to the Sith, could be a main character. This student might be initially unaware of their connection to the Sith Academy but starts to have strange visions and powers. As they explore their heritage, they end up at the Sith Academy, where they have to decide whether to embrace the dark side or use their knowledge to bring about positive change. Draco Malfoy could also be a main character in this scenario, as his family's interest in power might draw him to the Sith Academy in some way.
Harry Potter himself would likely be a main character. He's the central figure in the Potter universe. And maybe Darth Vader or another Sith Lord could be a major part of it too. As for the harem, Hermione and Ginny from the Potter side could be part of it, along with some female Sith characters, like Asajj Ventress if we're including Star Wars elements.
Maybe Neville Longbottom's younger cousin. They grow up hearing Neville's stories and are inspired to search for treasures that are related to the Battle of Hogwarts. They are brave and curious, and they start their hunt with a determination to discover something that can further the legacy of Hogwarts.
A half - blood wizard who has grown up in the seedy underbelly of the wizarding world and has learned all the tricks of the trade. He has a rough exterior but a good heart deep down.
Harry Potter himself could be a main character. Imagine him using his Gryffindor courage to take on the most dangerous monsters in the Monster Hunter world. He could combine his magical abilities like his flying skills on a broom with Monster Hunter strategies.
One interesting concept could be the combination of the magic from the Harry Potter universe and the Sith hunting element. Maybe the characters use spells like in Harry Potter to track and combat the Sith. For example, a Patronus charm could be used to repel the dark side influence of the Sith.
Perhaps a new type of creature that is neither from the Harry Potter world nor the Witch Hunter's world. It could be a result of some dark magic experiment gone wrong. This creature could have the ability to nullify magic in some ways, which would be a huge threat to both Harry and the Witch Hunter.
Obviously, Harry Potter himself could be a main character. He could be the one who bridges the gap between the two worlds, using his skills in magic and his courage to face the challenges of the Monster Hunter world. Hermione would also be a great main character. Her intelligence would help in understanding the new creatures and the Monster Hunter techniques. And perhaps a Monster Hunter from the Monster Hunter world could be a main character too, guiding Harry and his friends in that world.