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.
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 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.
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 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.
One possible plot development could be Hanabi trying to get closer to Naruto. She might start by finding excuses to be in the same place as him, like showing up at his favorite training spots. Another could be her trying to impress Naruto with her skills, perhaps by showing off her new jutsu in front of him. And she could also start to compete with Hinata in a friendly way for Naruto's attention.
A plot development might involve Naruto struggling to control the Rinnegan at first. Sasuke, noticing this, believes he can defeat Naruto easily with his Sharingan. But as Naruto starts to master the Rinnegan, he shows new abilities that shock Sasuke. This could lead to a situation where they have to team up against a common enemy who is after the power of both the Rinnegan and the Sharingan. Or perhaps a prophecy is revealed that states only one of them can keep their dojutsu power and they must fight to decide who keeps it, leading to a moral and power - based struggle.
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 the 'naruto has no eyes fanfiction', the plot might involve Naruto discovering a new form of chakra that is unique to his condition. This new chakra could give him abilities that he didn't have before, like the ability to sense the emotions of his opponents. There could also be a plot twist where Naruto's blindness is actually a part of a greater prophecy, and he has to fulfill it in a way that no one expected.
A plotline might involve Naruto starting to act out in negative ways to get his parents' attention. He could start getting into trouble at school or in the village. Maybe he would start to explore his own powers in secret, away from his family, and discover some unique abilities that he then uses to show his parents what they've been missing. Also, there could be a plotline where Naruto tries to build a relationship with his sister in secret, hoping that through her, he can get closer to his parents.
Well, perhaps in this fanfiction, Naruto is somehow transported to the Batman universe and is neglected by the local heroes at first. He then has to prove himself by using his ninja skills in Gotham's dark alleys, like using his shadow clones to confuse the bad guys and his speed to catch the elusive criminals.