How about a story where a pony princess has a vision of the pirate world in trouble. She sends a group of ponies as ambassadors. These ponies meet the pirates and they soon find out that a powerful sea monster is terrorizing the pirates. The ponies use their magic to try and defeat the monster. In the process, they form unexpected friendships with the pirates. There could be some really fun scenes of ponies trying to navigate a pirate ship and the pirates being in awe of the ponies' magic.
One idea could be that the RWBY characters find themselves on a cursed ship similar to the ones in Pirates of the Caribbean. Ruby could be the fearless leader, using her scythe in sword - fights on the ship's deck. Weiss might be the one trying to figure out the magic or curses involved, with her knowledge of Glyphs. Blake could use her stealth skills to explore the ship and discover hidden secrets, and Yang would be the muscle, ready to take on any enemy pirates.
One idea could be a crossover with 'Peter Pan'. The pirates could sail to Neverland and have adventures with Peter, Tinker Bell and the Lost Boys. Maybe Captain Jack Sparrow would try to steal the fairy dust from Tinker Bell.
One way to combine them could be through a magical portal. Maybe Twilight Sparkle discovers a spell that opens a portal to the world of Pirates of the Caribbean. Then, the ponies could interact with the pirates. For example, Rainbow Dash might be fascinated by the pirate ships and their ability to sail fast. She could team up with Jack Sparrow, with her speed and his wits making for an interesting duo.
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.
Another plot could involve Elizabeth Swann time - traveling. She gets sent to a future version of the Caribbean where piracy has been completely eradicated. However, she discovers that without pirates, the balance of power in the region has been thrown off and there are new tyrannical forces at play. So, she has to find a way to bring back the spirit of piracy in a more civilized way to restore the balance. She uses her knowledge from the past and her wits to start a revolution of sorts.
One interesting plot could be the human adjusting to the magical world of Equestria. For example, learning to use magic or getting used to the different species and their cultures. Another idea is the ponies trying to understand human behavior and needs. They might be confused by things like human technology or the lack of a horn or wings.
One interesting plot idea could be a mystery during the wedding. For example, a valuable item goes missing right before the big moment. Another could be a character from the guests' past shows up unexpectedly and has some unresolved issues with the bride or groom. A third idea might be that there are some magical mix - ups that cause comical chaos during the ceremony.
A really interesting plot could be a pony from the other side who has unique powers that are considered dangerous in their own world. They flee to the normal pony world and have to hide their powers while also trying to find a place where they belong. This could involve a lot of character development as they interact with the normal ponies and learn about a different way of life.