One possible plot could be that Naruto gets sick with a cold, but because he's often neglected by the villagers, no one really notices or helps him. He has to struggle through it on his own while still trying to keep up with his ninja training. It could show his determination and how he overcomes even when he's physically weak.
Perhaps there is no traditional 'big bad' antagonist. Instead, the antagonist could be the overall neglect and apathy of the village itself. It's like the village's indifference towards Naruto when he's sick with a cold is the force he has to fight against. He has to break through this wall of neglect to get the care and respect he deserves.
Perhaps he's been influenced by someone who gives him bad advice. For example, if someone tells him that natural talent is enough and training is overrated. Also, he could be dealing with some personal problems, like a conflict within his family or among his friends that takes up all his time and mental energy, causing him to neglect training.
He might start to rely on his friends more. For example, Sasuke and Sakura could become his main source of emotional support. He would focus on training with them and sharing his feelings, which in turn helps him to grow stronger and more independent.
In Naruto, the Jinchuuriki were often treated poorly. In fanfiction, this neglect can be explored in many ways. One common approach is to focus on the emotional and psychological impact on the Jinchuuriki. For example, they might feel isolated from the rest of the village due to the fear and prejudice associated with the tailed beasts within them. This can lead to some really interesting character development stories in fanfiction.
In a fanfiction, perhaps neglected Naruto runs away from Konoha and ends up in the same area as Yugito. Yugito, having also faced her own share of hardships, takes Naruto under her wing. They bond over their experiences, and Yugito helps Naruto to better understand his chakra nature by sharing her knowledge of the tailed beasts' chakra. This could lead to Naruto developing new abilities and a newfound confidence.
One reason could be that some fanfiction authors might focus more on other aspects like new jutsu or character relationships outside of the Uchiha clan. They may not fully understand the potential of Sharingan, which has a wide range of abilities from basic perception enhancement to powerful genjutsu. Another factor could be the over - popularity of some other elements in the Naruto universe, like the tailed beasts, which overshadow the Sharingan in their stories.
I'm not sure specifically as I haven't read this fanfiction. But generally, if Harry is 'neglected', it might explore how being ignored or overlooked affects him in the context of Ravenclaw house in the Harry Potter universe. Maybe it shows his struggle to fit in or prove himself among the Ravenclaw students.
It might be explored through lack of training or guidance. Since he's godlike, the village might think he doesn't need any help. So, they neglect his development in terms of combat strategies or new jutsu, leaving him to figure things out on his own.
The angel bloodline might be neglected in the fanfiction due to the lack of connection to the existing Naruto lore. In the Naruto world, there are already established power systems and lineages. If the angel bloodline is not carefully tied to these existing elements, it may be pushed to the side. Additionally, the writer might be saving it for a big reveal later in the story, so it appears neglected in the early parts.