Well, identity is a big theme. Since the female protagonist is in a world mainly presented with a male lead in the original, exploring her own identity within that context is common. Also, there's the theme of justice. She, as a Phantom Thief, is fighting for justice in the fanfictions, just like in the game. There can be sub - themes related to her unique perspective on the targets they steal from, as she might approach them differently than the male lead would.
One of the main themes is her growth as a character. The fanfiction often delves into how she becomes stronger, not just in terms of combat abilities with her Persona, but also mentally and emotionally. For instance, how she overcomes the fear of losing her friends in battles against Shadows. Also, the theme of sacrifice is common, as she might have to make difficult choices to protect the world she lives in, similar to what she does in the game.
Joker is often paired with the female protagonist. Their relationship can be explored in different ways, from being comrades in the Phantom Thieves to having a more romantic connection. Ryuji is also a popular choice as they can have a fun, energetic dynamic.
One idea could be exploring her relationships with the other characters in more depth. For example, how she bonds with Yosuke, Chie, and Yukiko outside of the main plot. Another idea is to create an alternate universe where she has different Persona abilities or a different backstory that changes the way she approaches the Midnight Channel mystery.
A popular pairing is with Yu. They both are the main characters and have a lot in common in terms of their roles in the story. Their relationship could be explored in a romantic or a deep platonic way. Another good pairing could be with Naoto. Since Naoto is also a very unique character, the two of them could bond over their different perspectives and skills, and there could be a great dynamic between them.
One interesting plot could be the female protagonist forming a special bond with a new confidant not in the original game. This new relationship might lead to unique story developments, like uncovering a hidden mystery in the Metaverse that was overlooked before.
One popular theme is friendship. Fans often explore the relationships the female protagonist forms with other characters in the game. Another theme could be self - discovery, as she navigates the strange world of Persona. And also, adventure stories are common, where she goes on quests and battles Shadows.
Morgana is very common. He's always by the protagonist's side in the game, so he often plays an important role in fanfics too. Ryuji is also frequently seen. His energetic and sometimes reckless nature provides an interesting contrast to the female protagonist. And Ann, with her beauty and kind heart, is often included as a good friend or ally.
There are fanfictions that put the female protagonist in alternate universes. She might be in a modern - day high school setting without the threat of Shadows, just living an ordinary life but still having the traits that made her so beloved in the game. Or she could be in a crossover with another game or series, like teaming up with characters from 'Persona 5' which would create really interesting dynamics.
The fanfiction can incorporate Persona 5 themes by exploring the concept of the Metaverse. Imagine that Neverland has a hidden Metaverse layer. The female character from Persona 5 discovers this and has to navigate it. In this Metaverse - like Neverland, she uses her Persona skills to uncover secrets and solve mysteries. The power dynamics between different characters in Neverland can also mirror the power struggles in Persona 5, such as the fight against the corrupt adults in the game.