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.
It could also be that the sister, in an attempt to help Naruto, gets involved with some dangerous characters or situations. Maybe she tries to find someone powerful to plead Naruto's case, but that person has some ulterior motives. This would add a lot of twists and turns to the story, as Naruto then has to not only deal with his own problems but also save his sister from the trouble she has gotten into while trying to help him.
A plot development could be that Kakashi discovers the root cause of Naruto's neglect. It might be related to some hidden secrets in the village. Then Kakashi has to fight against those who are behind Naruto's neglect while still training Naruto. Another development could be that Naruto and Kakashi form a very strong bond. Naruto then uses the skills and confidence he gained from Kakashi to face his enemies and also to try and change the village's attitude towards him.
One possible plot development could be that Naruto's friends in Konoha realize he's missing and start a search mission. They might suspect Kumo immediately due to the history of tensions between the two villages. Meanwhile, in Kumo, Naruto could be held in a secret location. Some in Kumo might want to use him as a bargaining chip against Konoha, while others might see his potential and try to turn him into an asset for Kumo.
One possible plot development could be Naruto exploring his new bloodthirsty nature and how it affects his relationships with his friends. Maybe at first they are scared, but then they try to understand him. Another could be Naruto seeking revenge on his family for neglecting him, which might lead to some intense confrontations. And finally, he could find a new family among his comrades who accept him for who he is.
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.
It could be that his sister has some special abilities or talents that the family or the village values more. For example, if she has a very rare and powerful bloodline limit, everyone's attention would be drawn to her. In a ninja world, power and potential are highly regarded, so Naruto might be overlooked because his sister seems to have more of that 'special something' at first glance.
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.
For Naruto, he could become more self - reliant. Since he's being neglected by Yugao, he might start to focus more on his own growth as a ninja and as a person. He could learn to not rely on others for emotional support as much.
In the 'naruto neglected by his mother fanfiction', Naruto may have a different approach to his ninja training. Instead of being motivated by the desire to be recognized like in the original story, it could be a way for him to escape from the pain of his mother's neglect. He might train harder and more recklessly, putting himself in danger because he doesn't really care about his own well - being as much, since he feels so unloved at home.
One possible plot development could be that the Sage discovers new powers within himself while being neglected. He might use these powers to prove his worth to the Kiri villagers who overlooked him. For example, he could save the village from a hidden threat, like a powerful and secretive enemy group that the regular shinobi of Kiri were unable to handle.