One idea could be that the ponies discover Pokemon eggs in Equestria. They start to raise the Pokemon and learn about their powers. For example, Twilight Sparkle could study the different types of Pokemon moves using her magic knowledge.
Maybe there's a portal that opens between the Pokemon world and Equestria. The Pokemon trainers come to Equestria and start trading Pokemon with the ponies. Ponies like Pinkie Pie would be really excited about the new friends and the idea of trading things.
One possible plot could be that some Pokemon accidentally end up in Equestria. The ponies are initially scared but then they realize the Pokemon are friendly. Together, they team up to stop an evil force that threatens both their worlds, like a powerful dark - type Pokemon and an evil unicorn. They use their combined powers of friendship and unique abilities to defeat the enemy.
One idea could be a crossover where Pikachu from Pokemon meets Twilight Sparkle from My Little Pony. They could go on an adventure together to save both their worlds from a common threat. Another idea is a story where the trainers from Pokemon enter the world of My Little Pony and have to adapt to the magical and colorful environment while also sharing their Pokemon skills.
A great concept for a Pokemon and My Little Pony fanfiction would be a race. Have some of the fastest Pokemon like Rapidash (which already has a pony - like appearance) compete against the Pegasus ponies in a grand race across different terrains. The story could focus on the training leading up to the race, the rivalries that develop between the Pokemon and ponies, and the unexpected friendships that form. Maybe a little Pony befriends a Pokemon and helps it train in a new way, using pony - style training methods that involve harmony and friendship.
One idea could be that the ponies discover a portal to the Pokemon world and start to form teams with the Pokemon they meet. They could learn about Pokemon battles and use their own unique pony abilities in combination with the Pokemon's powers.
Maybe some of the ponies from My Little Pony accidentally cross over to the Fairy Tail universe. They'd be amazed by the different types of magic there. The Fairy Tail guild members could help them understand this new world while also learning about the power of harmony from the ponies. For example, Twilight Sparkle could share her knowledge of magic with the Fairy Tail mages, and in return, they could teach her about their combat - oriented magic.
One idea could be that Naruto and his friends end up in the My Little Pony world. Naruto's energy and determination might be a bit of a shock to the gentle ponies at first. He could learn about the magic of friendship in Equestria, which is quite different from the chakra-based power in his own world. Maybe he'd team up with Twilight Sparkle to fight some common threat that somehow affects both their worlds, like a dark force that wants to steal both chakra and pony magic.
One idea could be that Dipper and Mabel end up in Equestria. Dipper might be intrigued by the magic there and start studying it, while Mabel could make friends with the ponies easily. Maybe they help the ponies solve a mystery that's been plaguing Equestria, like strange disappearances. Another idea is that a pony from Equestria somehow travels to Gravity Falls. It could be Twilight Sparkle, who is amazed by the different kind of 'weirdness' in Gravity Falls compared to Equestria.
One idea could be a pony being reborn with memories of a past life in a different pony world. They could use that knowledge to bring about positive changes in Equestria, like finding new ways to solve friendship problems.
One idea could be that the Dazzlings try to reform and join the main group of ponies in Ponyville. They struggle to overcome their past of using dark magic to steal harmony and learn to use their powers for good.
Well, a plot could involve a villain trying to steal all the cupcake recipes in Ponyville. The ponies then have to work together to protect their precious recipes. It could also be about a pony who has lost their sense of taste and has to go on a journey to regain it by trying different cupcakes. Or perhaps there's a mystery surrounding an ancient cupcake recipe that holds a great secret.