One common theme is the relationship between the cheerleader and Stiles. It often involves a budding romance or a strong friendship.
Another theme is the contrast between the cheerleader's more 'normal' school life and Stiles' often mysterious or supernatural - related situations. For example, the cheerleader might be part of the popular crowd while Stiles is dealing with things like werewolves or other supernatural entities, and how they bridge that gap is a big part of these fanfics.
Supernatural elements are also very common. Since the show is about the supernatural, fanfics usually include things like werewolves, witches, and other magical creatures. Stiles' interaction with these elements is always interesting to read about.
One common theme is the exploration of multiple relationships. Since it's a harem concept, there are several characters vying for the cheerleader's attention. Another theme is the cheerleader's own growth as she deals with all these relationships.
One common theme is friendship. Since Clarke is a cheerleader, she often forms close bonds with her fellow cheerleaders. Another theme is competition. There are usually rival cheerleading squads in the fanfic. For example, in many stories, Clarke's squad has to compete against others in championships.
One common theme could be friendship among cheerleaders. They often support each other through various challenges in the story. Another might be the pursuit of dreams, like winning a big cheerleading competition.
One common theme is power. Since Stiles is an alpha, the story often explores how he wields his power, whether it's for good or to face his enemies. Another theme is loyalty. His friends' loyalty to him and vice versa is usually a big part of the story.
One common theme is protection. Since Stiles is in a baby form, other characters often have to protect him from the various dangers in the supernatural world. Another theme is cuteness. Writers usually focus on the adorable things baby Stiles does like his little giggles or how he toddles around.
There are often themes related to empowerment. Fem Stiles may be portrayed as breaking gender norms within the Teen Wolf universe. For example, she could be shown as being just as good or even better at solving mysteries or fighting supernatural threats. Friendship is also a big theme. How her relationships with the other characters, like Lydia or Allison, change or stay the same in a different gender context can be an interesting exploration. Sometimes, there are also themes related to family, especially how her relationship with her father might be different as a female.
A common theme is adventure. Stiles often goes on quests in these ancient settings, exploring unknown lands. Another theme is discovery, like finding new cultures or magical elements.
One common theme could be the challenges and joys of impending parenthood. Stiles might face difficulties in preparing for the baby while dealing with his own life situations.
One common theme is the idea of redemption. Derek might be seen as a character who has a past to make up for, and Stiles helps him in that journey. Another is the theme of trust. They have to learn to trust each other despite their differences. And love, of course, is a major theme as their relationship develops.