A really cool plot would be if there was a fusion of Personas and Stands. Imagine a character having a Persona that has Stand - like abilities or vice versa. This could lead to some really unique battles and character development. The story could explore how these new hybrid powers affect the characters' personalities and relationships, and how they use them to fight against an evil force that is trying to merge the two universes in a way that would be disastrous for both.
One idea could be the Persona characters getting sucked into the JJBA universe. For example, the Phantom Thieves could end up in Morioh and have to deal with Stand users while trying to find a way back home. They might team up with Josuke and his friends to fight a common enemy that's causing chaos in both their worlds in a strange way.
One idea could be the characters from Persona 4 and Persona 5 swapping their worlds. So the Phantom Thieves end up in Inaba and have to deal with the Midnight Channel mystery. And the Investigation Team finds themselves in Tokyo and gets involved in the Metaverse. It would be really cool to see how they interact with the different environments and characters.
A crossover with a post - apocalyptic world setting. The Persona 3 characters find themselves in a world destroyed by some great cataclysm. They have to use their Personas not only to fight the Shadows that lurk in this new world but also to survive against other desperate survivors and new, mutated threats. They might also have to find a way to restore the world using their Persona powers.
A cool plot could involve a powerful Persona user from Persona 3 who has somehow lost their memory and ends up in Inaba (the setting of Persona 4). The Investigation Team from Persona 4 takes them in and tries to help them regain their memory. As they do, they discover that this person holds the key to preventing a major catastrophe that will affect both their worlds.
A great plot for Persona 4 crossover fanfiction could be a crossover with the 'Sword Art Online' universe. The Persona 4 gang could be trapped in the virtual world of SAO and have to use their Personas to defeat the bosses and escape. Or, they could cross over with the 'My Hero Academia' world. Here, they could attend the hero school and learn new ways to use their powers, while also sharing their Persona knowledge with the MHA characters. Also, a crossover with 'Harry Potter' would be interesting. They could attend Hogwarts and discover that their Personas have unique interactions with magic.
Maybe there's a situation where the Velvet Room attendants from Persona 3, 4, and 5 realize that there's a threat to the collective unconscious that only the combined efforts of the three protagonists can stop. So, they somehow manage to bring the characters together. The characters then start to learn from each other's combat styles and ways of forming bonds with their friends, which helps them in their fight. For example, the protagonist of Persona 3 could teach the others about his experiences with death and how to face it head - on in battle, while the Persona 4 protagonist could share his knowledge of reading people and finding the truth behind the mysteries. The Persona 5 protagonist could contribute with his skills in stealth and infiltration.
A really interesting plot could involve a new threat that emerges and can only be defeated by combining the powers and skills of the Persona 3 and 5 characters. For example, the combat styles of the two groups are different. The SEES members are more used to fighting in the Dark Hour, while the Phantom Thieves operate in the cognitive world. They would need to learn from each other's strategies. And on a character level, the more serious and reserved characters from Persona 3 could interact with the more flamboyant and confident characters from Persona 5, leading to some really interesting dialogue and relationship building.
A crossover with One Piece might also work well. Joseph Joestar could find himself on the Grand Line, interacting with the Straw Hat Pirates. His hamon abilities could be a strange and new power for the pirates to encounter, and he could help them out in battles against the likes of the World Government or other powerful foes, while also learning about the Devil Fruits and Haki.
Maybe the Velvet Room attendants from Persona start showing up in the Danganronpa setting. They offer the students a chance to awaken their Personas, but there's a catch - they have to face a series of trials similar to the class trials in Danganronpa. This could create a really unique and tense situation.
Maybe the Persona users' powers start to malfunction in the RWBY world due to the different nature of the place. So they have to figure out how to control their powers again while also helping the RWBY characters in their battles. The RWBY characters could be intrigued by the Persona powers and try to learn from them.
Maybe the Velvet Room attendants from both games somehow get their worlds mixed up. Igor from Persona 5 and Margaret from Persona 4 have to work together to set things right. This leads to the characters from both games interacting. The Phantom Thieves might learn some new combat techniques from the Investigation Team and vice versa. They could then use these new skills to face a common threat that emerges from the merging of their two realities.