Well, obviously Naruto himself is the central character. Sasuke is often included as his rival. Their relationship in these fanfics can be complex, with Sasuke either being suspicious of Naruto's new - found strength or being inspired by it. Sakura might also be there, trying to figure out what's going on with Naruto and how he got so strong all of a sudden.
Well, it depends on the specific fanfic. There are countless fanfictions out there, and some might indeed have a plot where Naruto has a secret connection to the Uchiha clan. Maybe it's a result of some hidden family ties or a magical spell that makes him related to them in some way.
One possible plotline could be that Naruto has been secretly training with an ancient sage. This sage has taught him unique jutsu that no one else knows. For example, a jutsu that can manipulate time on a small scale during battles, which gives him an edge without others suspecting.
Well, Naruto is obviously one of the main characters since it's about Naruto secretly being a girl. And Sasuke would also be a key character as Naruto's relationship with him is a significant part of the Naruto story in general.
They are popular because it gives a fresh take on Naruto's character. Instead of the typical 'dumb but strong' perception, it shows his hidden intelligence, which makes the character more complex and interesting.
Maybe some of the Akatsuki members could be his secret allies. For example, Itachi might have had a secret plan and saw Naruto's potential, so he was secretly helping Naruto become stronger all along. Also, there could be some minor characters from other villages who have recognized Naruto's hidden power and decided to ally with him.
One reason could be for the sake of creating unique power dynamics. If Naruto is an Uchiha, he could potentially have access to the Sharingan or other Uchiha abilities, which would make his battles and character development very different.
Maybe there's a plot where Naruto, as a girl, has to face unique challenges in her training. She might have to prove herself even more in a male - dominated ninja environment, which could lead to some inspiring stories of her overcoming gender - based obstacles.
One common theme is unrequited love. Often, Sasuke is shown as having these secret feelings while Naruto is oblivious. Another theme could be the struggle between Sasuke's pride and his feelings for Naruto. He might try to hide his emotions because of his Uchiha pride or his past traumas.
There are fanfics where Naruto is secretly a master strategist. He might pretend to be the clueless knucklehead but in reality, he has carefully planned every move. This can add a whole new layer of depth to his character and the story. He could be secretly guiding the actions of his team, making them think they are coming up with the plans on their own.