Well, in some fanfictions of this kind, Naruto's sister is often portrayed as having a special bond with him. She might have a unique ability that she uses to shield Naruto from the emotional pain of being neglected. For example, she could have a power to absorb negative emotions, and whenever Naruto is feeling down because of the neglect, she uses this power to make him feel better. There are also stories where she tries to expose the unfair treatment Naruto is getting to the village elders, but has to be very careful as she doesn't want to put Naruto in more danger.
It's popular because it explores a different side of Naruto's story. The idea of him having a sister who cares when others don't adds an interesting dynamic. People like the concept of family loyalty and the sister being a support system that Naruto was lacking in the original story.
One example could be a story where Naruto is so focused on becoming Hokage that he unintentionally neglects fem Sasuke. She might start to feel left out and lonely. In such a fanfiction, the author could explore her feelings of abandonment and how she tries to get Naruto's attention back.
One good example could be a fanfic where Naruto is a prodigy in a particular jutsu but is neglected by the village elders. In this type of fanfic, Naruto might secretly train and develop his skills on his own. For instance, he could be a prodigy in space - time ninjutsu but is not given the proper resources or guidance. Another example might be a story where he is a prodigy in medical ninjutsu but is overlooked because of his status as a jinchuriki. Fanfics like these often explore Naruto's character in a different light, showing his determination to rise above the neglect and prove himself.
In some Naruto neglected vampire fanfictions, the vampire might be a former enemy who is now trying to live among the ninja. However, they are constantly overlooked or feared. For instance, they could have the ability to turn into a bat, which is a cool power but causes others to be suspicious of them. This kind of fanfiction often explores themes of acceptance and isolation.
One example could be a crossover where Naruto is neglected in a world of Fairy Tail. Maybe Naruto is transported there but because he doesn't have the same type of magic as in that world, he's initially overlooked and neglected. Another could be a Naruto and Bleach crossover where Naruto's unique skills are not recognized at first, leading to his neglect. There could also be a crossover with One Piece where Naruto's ninja abilities seem out of place and he's not given much attention at the start.
Another storyline could involve Naruto's sister being trained more rigorously by the village elders because they see more potential in her. Naruto, feeling neglected, then goes on a self - discovery journey to find his own strength outside the village's traditional training methods. As he grows stronger, his sister realizes the mistake of the elders and tries to make it up to Naruto.
In such a fanfiction, perhaps the village's needs are always put first by Naruto, and his sister gets the short end of the stick. For example, he might not be there to protect her when she faces some bullies in the village just because he's too busy with village affairs. This could cause her to doubt Naruto's love for her, and she might even consider leaving the village in search of a place where she feels more valued.
Another aspect could be the relationship between Naruto and his sister. If she is the favored one, she might initially be oblivious to Naruto's pain. But as the story progresses, she could realize how wrong it is and try to make it up to him. This could lead to a complex family dynamic exploration in the fanfiction.
One example could be a fanfic where the samurai are left out of important village decisions in the Naruto world. They are often overlooked in favor of the shinobi, and a fanfic might explore how this makes them feel and what they could do to gain more recognition.
One example could be a fanfiction where Naruto is neglected by his friends in the Hidden Leaf Village after a major event, and he starts to develop some rather extreme and uncharacteristic behaviors as a result. Maybe he becomes overly distrustful and starts to isolate himself, which is a far cry from his normal, positive self.