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 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.
One idea could be that Naruto finds himself in a universe where the Akatsuki are the heroes. He has to figure out how to co - exist or even join them to get back to his own universe. Another plot could be Naruto entering a universe where everyone has a different elemental chakra, like some have sound - based chakra instead of the usual five. A third idea is that he hops into a universe where the shinobi world is a utopia, but there are hidden secrets that are threatening to destroy this perfect world and he has to help.
In the 'naruto juubi alternate universe fanfiction', it would be interesting if the characters' relationships were reversed. Like Sasuke could be the one trying to protect Naruto who has the Juubi's power, because he realizes that Naruto's power is the key to a new world order that could benefit all ninjas.
One interesting plot could be if Harry was sorted into Slytherin instead of Gryffindor. It would completely change his relationships and how he's perceived. He might have to deal with the prejudices of his own house while also trying to figure out his role in the fight against Voldemort.
In a Dragon Ball alternate universe fanfiction, there could be a plot where all the Saiyans survived the destruction of Planet Vegeta. They form an alliance with Earth and together they face new threats from a different galaxy. This would change the power dynamics completely. There could also be a scenario where the Kaioshin are the main antagonists. They use their divine powers in a corrupt way, and the Saiyans and Earthlings have to join forces to stop them. And what about a universe where the concept of ki is different? Maybe it can be transferred between people like a currency, and battles are fought not just with strength but also with strategic ki trading.