Well, you could have a story where the Pokemon are being affected by the Darkness from Kingdom Hearts. Some Pokemon start to turn into dark versions of themselves, similar to the Heartless. A young trainer, along with a Kingdom Hearts character like Riku, tries to find a way to purify these Pokemon. They could travel to different regions in the Pokemon world, facing challenges and battles along the way. The trainer could learn some of the skills that the Kingdom Hearts characters use, like using magic to enhance their Pokemon's abilities in battle.
One idea could be a crossover where Sora and his friends from Kingdom Hearts end up in the Pokemon world. They could team up with trainers to battle against the Heartless that have somehow invaded the Pokemon realm. Another idea is that some Pokemon could have the power of Keyblades, and they use it to protect their regions from both Pokemon villains and the threats from Kingdom Hearts like Organization XIII. Maybe a Pokemon like Pikachu could befriend Sora and they go on an adventure together to find a way to get Sora back to his own world while also helping the Pokemon world.
One idea could be a story where the Pokemon trainers are transported to the Kingdom Hearts universe and have to team up with Sora and his friends to fight against the Heartless. They could use their Pokemon's unique abilities in combination with keyblades to defeat the enemies.
One idea could be that Tangela gets transported into the Kingdom Hearts universe and has to team up with Sora to find a way back to its own world. Along the way, Tangela discovers new powers that are a combination of its Pokemon abilities and the magic in the Kingdom Hearts world.
Another interesting concept is an OC who is a member of an organization that opposes Organization XIII in a different way. Maybe they use magic that is not based on darkness or light, but something in between, which causes them to be shunned by both sides at first.
One idea could be exploring the backstories of the new characters introduced in Kingdom Hearts 3 in more depth. For example, you could write about how they came to be in the different worlds and what their true motives are.
One idea could be a fanfiction where the characters from Kingdom Hearts watch their own adventures from an alternate universe. It would be really cool to see their reactions to different versions of themselves and the events that unfold.
Well, some might explore unique character relationships that deviate from the original game's relationships. For example, it could create new storylines where the 'futa' characters interact with male characters in ways that add depth to their personalities and the overall plot.
One idea could be to explore what would happen if Sora and his friends got trapped in Ariel's underwater world during a Heartless attack. They'd have to team up with Ariel and her friends to fight off the Heartless while also dealing with Ursula's schemes in a new way.
One idea could be that Sora and his friends end up in Equestria. They could team up with the ponies to fight a new threat that is affecting both their worlds. Maybe the Heartless are somehow being drawn to Equestria's magic and they need to find a way to stop it together.
One idea could be creating an OC who is a keyblade wielder from a forgotten world consumed by darkness. This OC could be on a journey to find a way to restore their world while also struggling with the allure of the darkness within them.
One idea could be that the Heartless somehow find their way into the Marvel universe and start attacking various locations. The Avengers, being the protectors, team up with Sora and his friends from Kingdom Hearts. They initially have some clashes due to different fighting styles and ways of understanding the world, but eventually learn from each other and combine their powers to defeat the Heartless. For example, Iron Man could use his technology to analyze the Heartless' weaknesses, while Sora uses his Keyblade to directly combat them.