How about a crossover with Disney characters? Picture the Equestria Girls meeting the Disney princesses. They could all have a ball together and share their different stories of heroism. Rarity would probably be in awe of the beautiful gowns the princesses wear and might try to create her own versions inspired by them.
A crossover with the Winx Club. The fairies from Winx Club could come to the Equestria Girls' world and they could have a magical battle tournament. Each side could learn new spells and techniques from the other. Maybe the Equestria Girls could learn some new flying techniques from the Winx Club fairies.
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.
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.
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.
A cool fanfiction concept could be a crossover tournament. Ben 10 brings some of his alien allies, and the Equestria Girls bring their friends from Canterlot High. They compete in a series of challenges that test both strength and magic. Each team has to learn from the other's abilities and work together at times. This could lead to some interesting friendships and rivalries between the characters from the two different universes.
One idea could be that Harry, with his magic skills, ends up in the Equestria Girls' world and helps them solve a mysterious magical problem that their normal magic can't handle. For example, a dark spell is cast over the school and only Harry's unique brand of magic can break it.
One idea could be that your self - insert character is a new student at Canterlot High. They have a special talent for art but are really shy. As the story progresses, they get involved with the main characters like Twilight Sparkle and her friends. They help with a school art project that turns out to be a magical adventure. Another idea is that your character is a transfer student from a different dimension entirely and has unique magical powers that the Equestria Girls haven't seen before. This causes both excitement and some initial suspicion among the group.
One idea could be a crossover where Shadow meets the Equestria Girls during a magical event in their world. Maybe he has to team up with them to defeat a common enemy that threatens both his world and theirs.
One interesting story could be about a new student in Canterlot High who discovers she has a special power related to the Equestrian magic. This power helps her and her friends solve a mystery in the school.
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 possible plot idea could be Twilight Sparkle discovers a new magic power in the Equestria Girls world that is related to her futa form. This power could help her solve a mystery or overcome an enemy. Another idea is that she has to deal with the challenges of being different in this form while still trying to fit in with her friends. Maybe she could use her unique abilities to help her friends in unexpected ways, like using her newfound strength to protect them from a bully or a dangerous situation.
One idea could be a time - travel plot where the Equestria Girls go back in time to the founding of Canterlot High. They could witness the first magic being used there and have to ensure that history isn't changed too much. Another idea is a crossover with another magical school from a different franchise. For example, they meet students from Hogwarts and have to learn from each other's magic systems. And a third idea could be a story where they lose their magic and have to go on a quest to find a way to get it back, encountering many challenges and new friends along the way.