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.
Yosuke is often paired with the female protagonist. Their dynamic, which can range from friendly banter to a deeper connection, makes for interesting fanfic scenarios.
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 interesting plot could be the female protagonist exploring a new, mysterious dungeon that wasn't in the original game. It adds an element of surprise and adventure.
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.
There's a fanfiction called 'A Female Protagonist's Tale in Persona 5'. In this, the author delves deep into how the female lead might handle the challenges of the Metaverse differently from the male lead. It also has some great character development moments for her, like when she forms new Personas.