One interesting storyline could be a crossover where the RWBY characters find themselves on the Battleship Yamato. Maybe they have to work together to face a common enemy that threatens both their worlds. For example, a Grimm invasion on the Yamato's world.
Weiss, with her more refined upbringing, could initially be a bit shocked by the differences in the Yamato's world but would soon start to find ways to use her skills. She might help with strategic planning, using her knowledge from Beacon Academy.
One of the most intriguing storylines could be where Batman is interviewed about his first encounter with the Joker. It would give a deep insight into his thoughts and how that encounter shaped his view of Gotham's villains. Another interesting plot could be an interview that delves into Batman's relationship with his allies like Robin or Alfred. How he feels about their support and how it impacts his crime - fighting. Also, a storyline where he's interviewed about his no - kill rule and the moral dilemmas he faces when dealing with the worst of Gotham's criminals would be really engaging.
In this fanfiction, it could also be that Naruto is on a mission related to the battleship Yamato. There could be an evil force that wants to use the power of the Yamato for its own malicious purposes. Naruto has to team up with the ship's crew, which includes some characters with unique abilities of their own. They all work together, with Naruto leading the charge against the enemy using his Nine - Tails chakra and his vast array of ninja skills.
Naruto might be in awe of the battleship Yamato at first. He could use his chakra to enhance the ship's speed or power in some way. For example, he could transfer some of his chakra to the engines to make it move faster.
One interesting storyline could be Dark Naruto using the Rinnegan to reshape the ninja world according to his own dark vision. He might start by taking over hidden villages one by one, using the powers of the Rinnegan like the ability to summon powerful creatures or manipulate gravity. Another could be his interaction with other powerful characters. For example, how he would deal with Sasuke, who has his own set of powers and goals. It could lead to epic battles and power struggles.
Maybe a failsafe in a Young Justice fanfic could involve a character being put in a false reality as a safety measure. And the story could revolve around how that character realizes they are in a false world and tries to break free while the rest of the team is also trying to figure out what's wrong with their comrade.
One interesting storyline could be Belle trying to break Rumpelstiltskin's curse in a different way. Maybe she uses her intelligence to find a loophole in the magic. Another could be a story where they meet in a different realm and form an alliance before their usual story events.
Another great storyline might revolve around the ancient humans' unique cultures and societies. For example, their art, music, and religious beliefs. Fanfiction could explore how these aspects of their lives were influenced by their environment and the challenges they faced, like dealing with other alien species.
In some fanfictions, the Animalia aspect might involve Animagus forms. Snape could be an Animagus of an animal that has a special connection to Lily. Say he's a deer, which was Lily's Patronus. This would create a very unique and poignant dynamic in the story, as he would be symbolically closer to her in this form.
A great storyline might involve a fusion of the two worlds' mechanics. For example, the Velvet Room from Persona could have some connection to Joker's world. The Igor-like figure could offer Joker and his friends some new kind of power or knowledge that they use to combat a common foe. Or perhaps the Persona characters learn about Joker's Metaverse Navigator and try to replicate it in their world, which leads to all sorts of unforeseen consequences and adventures.