Well, one possibility is that Naruto could have unique powers related to the underworld. For example, he might be able to control shadows in a way similar to Hades' control over the dead. Maybe he could use his underworld - based powers to fight against the evils in the Naruto world. He could also have a connection to nature like Persephone, which would add an interesting twist to his character.
He might have a darker complexion, similar to the shadowy realm of Hades. His eyes could be a deep, almost black color, with a faint glow, representing his connection to the underworld. His hair might also have a slightly darker hue or even a bluish - black tint, like the color of a moonless night.
One way to develop the storyline could be to explore Percy's struggle with his new identity. Since Hades and Persephone are such complex deities, Percy might have a darker side to him. He could struggle with controlling powers related to the Underworld, like shadow manipulation or communicating with the dead. For example, in a school setting, he might accidentally let out some spooky manifestations when he's stressed.
I really like 'The Meeting of Seasons'. In this fanfic, the interaction between Persephone and Hades is so well - written. It focuses on how their different natures - her being associated with spring and life, and him with the underworld and death - actually complement each other. It's a shorter fanfic but manages to pack in a lot of emotion and character development.
Another theme is the duality of the underworld and the overworld. Fanfics often play with the idea of Persephone being a bridge between these two realms, and how her relationship with Hades affects both the light and dark aspects of the world.
One idea could be Percy discovering his unique heritage as the son of Hades and Persephone and struggling to fit in among the other demigods. He might have powers related to the Underworld that set him apart, like the ability to control certain types of plants that grow in the Underworld. Another plot could involve him having to deal with the politics between the gods because of his parentage. For example, Zeus might be suspicious of him due to his connection to Hades.
A major theme could be identity. Percy has to come to terms with being the son of two very powerful and different deities. It's not like being the son of Poseidon where he has a more straightforward heroic image. Here, he has to figure out who he really is.
One common theme is the power of love. Their relationship defies the norms of the Greek pantheon, and the fanfics often explore how their love overcomes all odds. Another theme is the duality of Persephone. She has a life in both the mortal world (on earth) and the underworld, and this is often explored in how it impacts her relationship with Hades.
A good 'Persephone x Hades fanfic' often has well - developed characters. For example, Hades should be more than just a dark, brooding figure. He could have his own insecurities and soft spots. And Persephone can be shown as a strong - willed character, not just a damsel in distress. Good descriptions of the Underworld and the overworld are also important as it sets the mood for their relationship.