The hunters could be antagonists. They might see the werewolf boy as a dangerous creature and try to hunt him down.
The Ministry of Magic could be a main antagonist. They have a history of being discriminatory towards werewolves. They might see Harry as a threat now that he's a werewolf and try to lock him up or restrict his movements. For example, they could pass new laws specifically targeting him, like making it illegal for him to attend Hogwarts as a werewolf.
Perhaps there is an ancient evil entity that feeds on the hatred between werewolves and vampires. It doesn't want Sasuke and Sakura to succeed in bringing peace. So it uses its dark magic to create misunderstandings and conflicts between the two, trying to keep them at odds and prevent any chance of unity.
In the 'woman werewolf tf story', it might be about a woman who has a family curse. Every generation in her family, one woman turns into a werewolf. She discovers this when she reaches a certain age. She has to deal with the secrecy from her friends and family who don't know about the curse. As a werewolf, she has enhanced senses that help her in some ways, like being able to sense danger from afar. However, she also has to constantly battle her inner wolf instincts that sometimes conflict with her human morality.
It could be other students at Hogwarts who sense something strange about Snape and his invisible friend. They might try to expose Snape's secret out of jealousy or because they think it's some sort of dark magic.
A new and original antagonist could be a rogue psychologist who has developed a powerful hypnosis technique. This character might be jealous of Peter's abilities and want to use hypnosis to take over his mind and use his powers for their own gain. Or it could be a secret organization that wants to use Peter as a weapon, and they use hypnosis as a means of control.
Another option is a group of demons who have a vendetta against Clary or the shadowhunters in general. They might use torture as a way to break her spirit and gain information about the shadowhunters' defenses.
The father of the baby could potentially be an antagonist if he has a different view on the pregnancy than Lucy. For example, if he wants her to have an abortion and she wants to keep the baby, he could create obstacles for her.
I don't know the exact details of this novel, but it could be other werewolves who oppose Dimitri's relationship with Madeline. Maybe they think it goes against the pack's traditions.
It could be other werewolf packs that see Lyla and Derek as a threat to their territory or power. Maybe they want to eliminate them to maintain their dominance in the werewolf world.
One possible theme is isolation. Since the boy is forsaken, he's likely to be alone and the story could revolve around his feelings of loneliness. Another theme could be identity. Discovering he's a werewolf means he has to figure out who he really is.