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.
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.
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.
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.
Well, one possibility is that Harry would face a huge internal conflict. On one hand, he's a wizard, on the other, he has this heritage of a witch hunter in his blood. He might struggle with the idea of magic being 'good' as he's been taught all his life by the wizarding world that magic is wonderful, but his witch hunter ancestry could make him question it. Maybe he'd start to investigate the darker sides of magic more closely, trying to find a balance between what he's always known and what his heritage implies.
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.
Well, obviously, the hunter is one of the main characters. He's the one driving the story forward with his hunting - related adventures. There might also be some original characters created specifically for this fanfiction, like his mentor who teaches him the ways of hunting in the wizarding world. And of course, we could expect to see some of the familiar faces from the Harry Potter series, like Harry, Hermione, and Ron, who might interact with the hunter in different ways, either as allies or as people who are a bit skeptical of his methods.
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.
A lesser - known character like Ernie Macmillan from Hufflepuff could be the main character. As a prefect, he could bring out the unique qualities of Hufflepuff house. He might have to deal with issues like other houses underestimating Hufflepuff students. His story could focus on how he promotes the values of hard work, loyalty, and fairness within the house and the school as a whole.
Hermione could be a great main character. She's curious and intelligent, so she would be really interested in exploring the secrets of the diary. She could use her vast knowledge of magic to try and figure out how the diary works and what secrets it holds.