Well, Naruto is at the top of the list. Writers love to play with his character in different scenarios. Then there's Itachi. In alternate universe fanfics, we might see an Itachi who didn't have to make the difficult choices he did in the original story. And Sakura. She can be reimagined as a more skilled fighter from the get - go, without having to rely so much on her crush on Sasuke to drive her development.
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.
Well, in many Percy Jackson alternate universe fanfic, Leo Valdez is quite popular. People love to write about his inventions in different scenarios. Maybe he creates a super - powerful weapon that changes the balance of power between the demigods and the monsters. Grover also has his fans in these fics. He could be in a universe where he's the most powerful satyr ever and has to use his nature - related powers to save the world. And of course, Clarisse La Rue can be really interesting in alternate universes, like a Clarisse who teams up with her former enemies to fight a greater threat.
Hayato Gokudera is quite popular. In an alternate universe, he might be a lone samurai in a feudal Japan - like setting, or a tech - genius hacker in a cyberpunk world. Then there's Yamamoto. He could be a star athlete in a world where sports are the main focus instead of Mafia activities. His natural athleticism and positive attitude would make him a great character to develop in such a setting. Also, Hibari is often chosen. He could be the strict headmaster of a strict academy in an alternate educational - themed universe.
Severus Snape is a fan favorite in alternate universe stories. People are interested in seeing his character developed further, perhaps in a world where he didn't have such a complex relationship with Lily Potter. Harry Potter himself is, of course, a popular choice. Fanfic writers might create scenarios where Harry discovers his magic much earlier or has different adventures outside of Hogwarts that change his character development.
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.
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.
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.
In alternate naruto fanfiction, Hinata can be extremely popular. Writers might give her a more assertive role. For example, in some stories, she could be a powerful leader instead of the shy girl in the original series. Also, Itachi is a popular choice. His complex character and the mystery surrounding his actions make him ripe for exploration in alternate storylines, such as what if he didn't have to carry out the massacre of the Uchiha clan.
Edward is often still a very popular character in reimagined fanfiction. Writers might give him new backstories or tweak his personality slightly. For instance, he could be more rebellious against the vampire coven rules.