Maybe Elizabeth discovers a prophecy about Minato and she becomes determined to protect him at all costs. This could lead to a lot of action - packed scenes as well as some really tender moments between them. For example, when she has to shield him from a powerful enemy attack.
Another plot idea is that Minato loses his memory and Elizabeth has to help him regain it while also trying to keep their relationship intact. Along the way, they meet various characters from the game who either help or hinder their progress. This would give a chance to explore different aspects of their personalities and how they interact with others in the context of their relationship.
Through shared experiences. For instance, they could participate in a special event in the game world that forces them to trust and depend on each other. This would be a great start to developing their relationship.
A possible plot could be that there is a strange energy disturbance that starts to merge the three universes together. Characters like Ragna from Blazblue, the Persona users, and Team RWBY find themselves in a strange new world that is a mix of all three. They must figure out what is causing this and how to stop it. Maybe there are also new enemies that are created from the combination of the different mythologies and technologies of the three universes. For instance, Grimm with the ability to use Persona - like powers or Blazblue - style Ars Magus. It would be a great opportunity for character development as they learn to work together despite their differences.
A more action - oriented plot could involve Yu and Naoto being targeted by a new enemy that is related to the Shadows. They have to use their Personas together to fight this new threat. During their battles and the time they spend preparing for them, they grow closer. Yu might use his natural leadership skills to protect Naoto, and Naoto's intelligence could help them strategize. This shared danger could bring out their feelings for each other.
Another idea is a crossover with a superhero universe. Minato could find himself in a world full of superheroes and villains. He'd have to figure out how his Persona powers work in this new context. Maybe he teams up with some heroes to fight a common enemy, like an evil entity that threatens both his world and the superhero world.
Another option is a crossover with the Pokémon world. The Phantom Thieves could travel to a region in the Pokémon world and discover that someone is using Persona powers to make Pokémon act out of control. They would need to catch Pokémon themselves and use their combined powers of Personas and Pokémon to stop the bad guy. It would be interesting to see how they interact with Pokémon trainers and the whole Pokémon ecosystem.
A cool plot could involve the Persona 5 crew going back in time to the events of Persona 3. They might end up interfering with some of the original events, which could have unforeseen consequences. For example, they could accidentally change the way a key character in Persona 3 awakens their Persona, and then have to figure out how to fix it while also dealing with the Shadows in that era.
One idea could be to cross it with another popular RPG. For example, having the Persona 4 characters enter the world of Final Fantasy. They could interact with the different races and magic systems there. Another could be a crossover with a detective - themed anime. The Investigation Team could team up with the detectives from that anime to solve a mystery that spans both worlds.
A great plot could involve the transfer of Personas between the two groups. For example, a character from Persona 3 accidentally gets a Persona that belongs in the world of Persona 4 and vice versa. This causes chaos as they have to learn to control and understand these new entities while also dealing with the reactions of their respective teams.
Well, an interesting plot could involve an OC that is a transfer student, just like the protagonist. But this OC has a hidden past related to the Metaverse. Maybe they were experimented on by a shadowy organization in their home country, and this gives them a different perspective on the Metaverse compared to the Phantom Thieves. Their goal could be to find out who was behind those experiments and get revenge. Along the way, they form a bond with the group and learn new ways of using their powers.
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.