Maybe the trainers from the Pokemon world end up in Equestria. They could introduce the concept of Pokemon battles to the ponies. Some ponies might be interested in learning how to be trainers themselves, while others might be more concerned about the safety of their land with these new and potentially dangerous Pokemon around.
One idea could be that the Pokemon are discovered in the world of MLP. The ponies could be both amazed and a bit scared at first. For example, Pikachu's electric powers might seem like a strange and powerful magic to them. They would have to figure out how to interact with these new creatures.
Another concept could be a fusion of Pokemon and ponies. A Ponyta could have some unique abilities of a certain Pokemon, like being able to use water - type moves if it was fused with a water - type Pokemon. This would create new and exciting characters and storylines as the characters explore their new powers and identities.
One idea could be that the ponies from MLP accidentally enter the Pokemon world through a magical portal. They team up with some Pokemon trainers to stop an evil team that's trying to use both pony magic and Pokemon power for their own bad deeds. Another plot could be a Pokemon tournament where ponies are allowed to participate using their unique abilities as if they were Pokemon. For example, a Pegasus pony could use its flying skills in a battle like a Flying - type Pokemon.
A cool fanfiction idea is a story where a legendary Pokémon ends up in Equestria. For example, Mewtwo could arrive and the ponies initially fear it due to its power. But then they realize Mewtwo is just lost and confused. The ponies, with their kind hearts, try to help Mewtwo find its way back home. Meanwhile, the Pokémon could learn about the magic and friendship in Equestria.
In Pokemon and MLP crossover fanfiction, the idea of Pokemon living in the Equestria from MLP is quite cool. Some Pokemon might fit right in, like the grass - type Pokemon that could interact with the natural environment there. And then there are the battles. Instead of the normal Pokemon battles, they could be adapted to fit the more magical and less violent nature of MLP. Maybe instead of fainting, a Pokemon just gets tired and needs some magical energy to recover. And the different Pokemon forms could be seen as different 'levels' of magical creatures in the eyes of the ponies.
One idea could be that Thomas the Tank Engine somehow ends up in Equestria. Maybe there's a magical portal that transports him there. He could then interact with the ponies, perhaps helping them with some big construction project like building a new bridge. The contrast between his mechanical world and the magical world of MLP would create a lot of comical and interesting situations.
One idea could be that the ponies from MLP end up in the Underground world of Undertale. Maybe Twilight Sparkle could use her magic to interact with the magical elements in Undertale, like the SOULs. Another idea is to have Sans and Papyrus meet Fluttershy. Papyrus would be all excited to show off his 'coolness' while Fluttershy might be a bit shy at first but then they could become friends over their love for cooking (Papyrus loves making spaghetti).
One idea could be that Godzilla somehow ends up in Equestria. The ponies are initially terrified but then realize Godzilla is more interested in protecting the land from some new dark force that has emerged there. Maybe Godzilla's size and power are a mystery to the ponies at first, and Twilight Sparkle tries to study him to figure out how he got there.
One idea could be Naruto characters suddenly finding themselves in the colorful world of MLP. For example, Naruto with his determination might inspire the ponies to face challenges bravely. He could teach them about the power of friendship in a different way, like how he values his bonds with Sasuke and Sakura. Another idea is a pony using Naruto - style jutsu. Picture a unicorn pony using chakra to perform a shadow clone jutsu to get more tasks done around Ponyville.
A possible plot could involve a dark force threatening both the world of Lucario and Equestria. A group of ponies and Lucario have to come together. The ponies use their magic and the Lucario use their combat skills and aura powers to fight off the common enemy. This would show how different abilities can be combined in a crossover story.
One idea could be a crossover with the Harry Potter universe. Pokémon could be integrated into Hogwarts, like having Pikachu as a familiar for a wizard. Another could be a crossover with the world of Final Fantasy. Pokémon trainers could team up with Final Fantasy characters to battle a common enemy. A third idea is a crossover with the Marvel universe, where Pokémon might have unique powers when exposed to the Infinity Stones.
One idea could be that Link, the hero from Legend of Zelda, somehow gets transported to the world of MLP. He might team up with Twilight Sparkle to fight against a common enemy that threatens both their worlds. Maybe Ganon has found a way to corrupt the magic in Equestria, and Link's combat skills along with Twilight's magic knowledge are needed to stop him.