One idea could be an alternate universe where the ponies have different elemental powers. For example, instead of Twilight Sparkle being a unicorn with magic related to friendship, she could control time. This would change the entire dynamic of the stories and the relationships between the ponies.
In an MLP alternate universe fanfic, it could be interesting if the roles were reversed. The villains could be the main characters trying to redeem themselves, while the traditional heroes are the ones causing trouble. It would give a fresh perspective on the MLP world and its values.
Another plot idea for an MLP alternate universe fanfic is a world where the ponies live in a post - apocalyptic setting. They have to fight against mutated creatures and find ways to restore harmony in a desolate land. This would introduce a darker and more challenging theme compared to the original MLP series.
Well, perhaps in this fanfiction's alternate universe, the Mane 6 are all from different species. Rainbow Dash could be a griffin, and they have to overcome the prejudices between their species to form their friendship. It could also be that they are in a post - apocalyptic Equestria, and they are on a quest to find the elements of harmony which have been scattered and lost.
Well, an interesting plot could be that the alternate universe is a post - apocalyptic world. The Vongola Guardians are now survivors trying to rebuild society. Tsuna has to use his leadership skills not in the context of the Mafia but in leading a group of people to find resources and fight off other dangerous gangs. Another idea is that the alternate universe has a different timeline. Some characters are from the future and some from the past, and they all come together in a time - warped situation that creates a whole new set of conflicts and alliances.
Well, in an MLP Dark Mirror Universe fanfic, a possible plot is that the Elements of Harmony are actually used for evil. The ponies who usually protect Equestria are now using the power of the elements to control and oppress others. There could also be a plot where the different pony races are at war with each other instead of living in harmony. Maybe the unicorns think they are superior and are trying to enslave the earth ponies and pegasi. And of course, the fanfic could explore how the friendships that were once strong in the normal Equestria are now broken in this dark mirror world.
One idea could be that in this alternate universe, Hufflepuff is the dominant house in Hogwarts. They have a secret society within the house that holds the key to an ancient magic that can save the wizarding world from a new, unknown threat. And the main character, a Hufflepuff student, discovers this by accident and has to take on the responsibility to gather the members of the society.
One idea could be a castle that floats in the sky in the alternate universe. It could be made of some kind of magical crystal that gives it the ability to levitate. The inhabitants of this castle might be a race of winged beings who use the castle as a base to protect their realm from dark forces.
You could start with a character from our world being mysteriously transported to the alternate universe and finding the castle. For example, a young archaeologist who was exploring an ancient ruin suddenly finds themselves in front of this magnificent castle. They then have to figure out how to get inside and what secrets the castle holds. This could lead to encounters with strange creatures and uncovering a plot that threatens both the castle and the alternate universe.
One idea could be a wedding between two ponies from different tribes, like a Pegasus and an Earth pony. They would have to overcome the differences in their cultures and traditions. For example, the Pegasus might have a flying ceremony while the Earth pony has a more grounded celebration. Another plot could involve a wedding planner pony trying to create the perfect wedding but facing all sorts of comical disasters along the way, like the flowers not arriving or the cake getting ruined.
One idea could be a Beezen character in the MLP world having to adapt to the magic there. Maybe they start off as an outsider and gradually learn to use the magic for good, like helping ponies build better hives or something.
One idea could be an alternate universe where the Fairy Tail guild is a secret organization in a steampunk world. The magic is powered by steam - powered devices and the characters have to adapt their powers to this new technology. For example, Natsu could use his fire magic to fuel steam engines in a more efficient way.
One idea could be a world where the darkspawn and the elves form an alliance. They might come together out of mutual desperation, the darkspawn seeing the elves' connection to the Fade as an advantage, and the elves seeing the darkspawn's numbers as a means to gain power and protection from the other races. Another plot could involve a Dragon Age universe where magic is completely outlawed. Mages would have to go into hiding, and templars would be more like a secret police force, leading to a lot of underground resistance and intrigue. A third idea is an alternate universe where the Qunari have taken over most of Thedas. Their strict way of life would reshape the cultures and societies of the other races in ways that are both fascinating and disturbing.