Well, Fluttershy is a character that shows up a great deal in fanfiction. Her gentle and shy nature gives writers a lot to work with, whether it's about her overcoming her fears or using her kindness to influence others. Applejack is also a favorite. Her loyalty and strong work ethic can be the focus of many stories, like how she manages the family farm. And of course, Rarity with her love for fashion and glamour is often written into fanfiction stories as well.
Yuu is definitely one of the most frequently written characters. His complex backstory and powerful ability make him an interesting subject. Nao is also popular as she is a strong - willed female character with her own set of abilities. Another character often written about is Joujirou, with his unique power and his role as a friend and ally in the story. Writers like to explore their relationships and develop their personalities further in fanfiction.
In many fanfictions, there's a Bat Pony leader character. This character is usually strong and wise, guiding the Bat Pony community. For example, a character like Shadowwing. Also, there are Bat Pony characters who are hybrids, part Bat Pony and part other magical creature. They tend to be popular as they have unique abilities and backstories. They can be both a source of intrigue and a bridge between the Bat Pony world and the rest of Equestria.
Van is definitely one of the most frequently written characters. He's the main character, and his journey, his powers, and his relationships are all very interesting to explore in fanfiction. Hitomi is also very popular. Her unique ability to see the future and her relationship with Van make her a central figure in many fan stories. Folken is another character often written about. His complex personality and his role in the story's conflicts attract a lot of fanfic writers.
Twilight Sparkle is often popular. Her intelligence and leadership skills in the original series make her a great candidate for reborn fanfiction. Writers can explore how she might use her past experiences in a new life to further her magical studies or help Equestria in different ways.
Twilight Sparkle is often very popular in fusion fanfiction. Her powerful magic makes her a prime candidate for fusions. When fused with other characters, she can bring a lot of intelligence and magical ability to the new entity. Rainbow Dash is also popular. Her speed and athleticism can add an exciting dynamic to any fusion she's part of.
Twinkle Twirl is often a beloved character. Her kind and gentle nature makes her a favorite in many fanfictions. Another one is Firefly. With her adventurous spirit, she gets into all sorts of exciting situations in the stories. And of course, there's also Cotton Candy, who is adored for her sweet personality.
Twilight Sparkle is also a favorite. Since she's so intelligent in the pony world, as a human she could be a top student or a young prodigy. People love to see how she uses her brains to solve problems in the human setting.
Twilight Sparkle is often very popular. Her intelligence and magic abilities make for great storylines, especially when she's dealing with the mysteries of a portal. Another popular one is Rainbow Dash, with her speed and bravery, she can have exciting adventures through the portals.
Queen Chrysalis is often a popular character. She has a strong presence and her villainous nature makes for interesting plotlines in fanfiction.
Twilight Sparkle and Naruto are often very popular. Twilight's thirst for knowledge can be a great parallel to Naruto's determination to become stronger. Also, Rainbow Dash with her athleticism can be compared to some of the more physically adept Naruto characters.