Well, in Danganronpa and Pokemon fanfiction, there might be a scenario where the Danganronpa students are transferred to the Pokemon world. They could then use Pokemon to solve the mysteries that occur there. Some students might be good at training certain types of Pokemon based on their personalities. Like Byakuya would probably have some rare and powerful Pokemon, like a Dragonite perhaps, as it suits his status - obsessed personality.
One interesting crossover could be the characters from Undertale finding themselves in the Pokemon world. For example, Sans could be wandering around the Kanto region, interacting with Pokemon trainers. He might use his unique abilities in battles against Gym Leaders. Another could be Frisk trying to catch Pokemon, but with their pacifist nature, they might have a different approach to Pokemon training, like befriending them without battling.
One interesting idea could be a crossover with a fantasy world like Middle - earth. Pokémon could interact with hobbits, elves, and dwarves. For example, Pikachu might befriend a hobbit and help them on an adventure. Another idea is a crossover with a superhero universe. Pokémon trainers could team up with superheroes to fight supervillains. And a crossover with a historical setting, like ancient Rome, where Pokémon battles are part of the gladiator games.
One interesting crossover could be a battle between Goku and a powerful Pokemon like Mewtwo. Goku's martial arts skills against Mewtwo's psychic powers would make for an epic showdown. Another could be Goku training with Pokemon to increase his speed and agility. For example, he might train with Pikachu to learn quick dodging techniques.
Maybe the Danganronpa characters get transported to the world of My Hero Academia. They then have to adapt to a world where having superpowers is normal. Some of them might try to use their unique skills from the Danganronpa world to become heroes or villains in this new setting.
One interesting crossover could be Ash and his Pokemon traveling to the Naruto universe and having to deal with the ninja world's challenges. Maybe Pikachu uses its electric attacks against ninja techniques.
Another idea in pokemon and harry potter fanfiction could be the sorting of Pokemon into Hogwarts houses. Some Pokemon, like Bulbasaur, with its calm and studious nature, might be sorted into Ravenclaw. While Pokemon like Charizard, which are brave and strong - willed, could end up in Gryffindor. This concept can lead to really creative stories about how Pokemon interact within the Hogwarts house system.
One interesting crossover could be the characters from Pokemon and Winx Club teaming up to fight a common enemy. For example, the fairies from Winx Club could use their magic in combination with the Pokemon's powers to battle a powerful dark force. Maybe Pikachu's electricity and Bloom's dragon fire could be combined for a super - attack.
In a Pokemon - Attack on Titan fanfiction, we might see the Titan - shifters having an unexpected connection with certain Pokemon. Perhaps Eren's Titan form could be influenced by a powerful and rare Pokemon. Also, the different regions of the Pokemon world could be incorporated into the Attack on Titan universe. Like the Johto region could be a place where some of the Scouts find a special type of Pokemon that has a unique ability to counter the Titans.
In some fanfictions, Ash might get access to one of Ben's Omnitrix-like devices. This could lead to him being able to transform into Pokemon - human hybrids, creating a whole new set of adventures and challenges. He could use this new power to understand Pokemon in a different way and face stronger opponents.
Another interesting crossover could be the appearance of Chaos Emeralds in the Pokemon XY world. Pokemon might be attracted to the powerful energy of the Chaos Emeralds. This could lead to a situation where both Sonic and Pokemon trainers have to protect the Chaos Emeralds from an evil force that wants to use their power to control both the Sonic universe and the Pokemon XY world.