Maybe there's a villain from the MLP world that follows them into the Equestria Girls world. The girls then have to team up with their Equestria Girls counterparts to defeat this villain. They could combine their different skills, like the pony Rainbow Dash's speed in the air and the Equestria Girls Rainbow Dash's skills on the track team.
Another plot could be that there's a magic item in the Equestria Girls world that is the key to solving a big problem in the MLP world. So the MLP characters go there to find it. Along the way, they make new friends among the Equestria Girls and learn about different ways of living and different values.
One idea could be that Sonic accidentally enters the world of Equestria Girls while chasing Dr. Eggman through a strange portal. He then teams up with the girls to stop Eggman from stealing the magic that powers their world. Another could be a race between Sonic and Rainbow Dash which gets interrupted by a common enemy.
One idea could be a human with unique skills, like being a great artist, arriving in Equestria. The ponies are fascinated by the human's different art style and the human has to learn about Equestrian art in return. For example, the human could introduce the concept of abstract art to the ponies, while learning about the magical paintings in Equestria.
One idea could be an OC who is a new student at Canterlot High. She has a unique power related to music, like she can make people feel different emotions through her singing. And she gets involved in a battle of the bands where there's some sort of mystery or magic influencing the competition.
One idea could be a crossover with another popular animated series like Steven Universe. The characters from Equestria Girls could visit Beach City and interact with the Crystal Gems. For example, Twilight Sparkle might be intrigued by Garnet's future vision ability and they could have a discussion about the nature of time and knowledge.
One idea could be a story about a new student arriving at Equestria Gakuen. This new character could be from a different part of Equestria and have to adjust to the unique culture and classes at the school. For example, if they're from a more rural area and come to a school in a big city in Equestria. Another idea is a fanfic centered around a school competition. Different groups of students form teams to compete in various magical and non - magical events, and there are lots of rivalries and friendships formed along the way.
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.
One idea could be that Discord causes chaos in Equestria that the MLP characters have to solve in a really wacky way. For example, he might turn all the clouds into cotton candy and the ponies have to figure out how to make it rain again without making a huge mess. Another plot could involve Discord getting his powers mixed up with a unicorn's magic and they have to work together to undo it. Maybe he accidentally gives Twilight Sparkle the power to turn things into random objects every time she tries to use her normal spells.
One interesting plot point could be the culture shock the Equestria Girls experience when they first arrive in Equestria. They might be amazed by the magic that is so commonplace there but strange to them. Another could be their interactions with the ponies. For example, they might have to learn new ways of communication and social norms.
Definitely Twilight Sparkle. In both worlds, she's a key character. In the MLP world, she's a powerful magic user, and in the Equestria Girls world, she can bring her intelligence and her problem - solving skills. Also, Rainbow Dash would be great. Her confidence and athleticism in both forms can create really exciting scenes, like when she races against the Equestria Girls' best athletes or uses her pony flying skills to save someone in a high - rise building situation in the Equestria Girls world.
Another plot could involve a villain that is a threat to both worlds. The Fairy Tail wizards and the MLP ponies would have to team up to defeat this common enemy. Maybe the villain is stealing magic from both worlds to become all - powerful. The ponies with their unique abilities and the wizards with their powerful spells would combine their forces in an epic battle.