I think Pinkie Pie remains popular in these fanfictions. Her wacky and unpredictable nature can be a great source of humor and chaos in an alternate universe. Fluttershy can also be quite popular as her gentle nature can be a contrast to the harsher elements of some alternate universes.
Twilight Sparkle is often popular. Her intelligence and ability to adapt can be really interesting in an alternate universe. Rainbow Dash is also a favorite. Her bravery and competitive spirit can lead to some exciting storylines in different universes.
Sasuke is often very popular in Naruto AU fanfiction. His complex personality and powerful abilities make him a great character to reimagine in different universes. Naruto himself is also a common focus, as writers like to explore different versions of him.
In Avengers alternate universe fanfiction, Steve Rogers is quite popular. He represents the old - fashioned values and strong leadership, which can be a great contrast or a source of conflict in different universes. Thor is also well - liked. Imagining him in different settings, like a more modern or a more magical alternate universe, is really fascinating. Natasha Romanoff is popular too. Her skills as a spy and her complex past can be the basis for many engaging stories in alternate universes.
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.
Daenerys Targaryen remains popular in alternate universes as well. She might have a different set of dragons, perhaps ones with even more unique abilities. Her conquest of Westeros could be either more brutal or more benevolent, depending on the fanfiction writer's vision, and her relationships with other characters could be completely reimagined.
The symbiote - Venom often has interesting interpretations in alternate universe fanfiction. In some universes, it could be a heroic entity instead of a villain, bonding with Spider - Man in a different way. Otto Octavius, or Doctor Octopus, also gets a lot of attention. In some alternate stories, he might be redeemed and become an ally of Spider - Man, or his origin could be completely different, like being a scientist from a parallel dimension.
In alternate universe Percy Jackson fanfiction, Percy is obviously a top character. People love to put him in various situations, like a world where he's a pirate. But Annabeth is right up there too. Her relationship with Percy and her own skills make her a key figure. Grover also has his fans. In an alternate universe where he has more magical abilities or is a different kind of nature spirit, he can be really interesting. And then there's Luke. Even in alternate universes, his complex character and his fall from grace are often explored, making him a popular character to include.
Marceline the Vampire Queen is another popular character. In alternate universes, she could be a different type of supernatural being or have a completely different backstory, such as being a guardian of an ancient and powerful magic instead of a vampire.
Rey is often a popular character in Star Wars alternate universe fanfic. Writers like to explore different paths for her, such as her training under different Jedi masters or her relationship with other characters in new ways. Kylo Ren is also popular. Fanfic authors might write about his redemption in more complex scenarios than in the official story. And of course, Darth Vader. There are always fanfics that imagine what would have happened if he had survived and changed his ways, or if he had different relationships with other Sith or Jedi in the alternate universe.
Naruto himself is often reimagined. Writers like to explore different versions of him, such as a Naruto with a darker personality. Sasuke is also popular. In some AUs, he could be a more carefree character. And Kakashi is another one. Maybe a Kakashi who didn't have to endure so much trauma at a young age.
Scully is also highly popular. Her scientific mind and her relationship with Mulder, whether it's changed or intensified in the alternate universe, are always interesting aspects for fans to write about. Sometimes she might be even more of a skeptic or more open - minded depending on the fanfic's concept.