One possible reason could be that they are too involved in their own shinobi duties. The world of ninjas is full of dangerous missions, and they might be constantly away on important tasks, leaving Naruto feeling neglected.
One plot twist could be that Naruto discovers his parents had a very good reason for their neglect, like they were protecting him from a greater danger. Another could be that the village elders knew about the neglect but did nothing, and Naruto has to confront them. Or perhaps Naruto finds out he has a secret power that was the cause of his parents' seeming neglect, as they were afraid of what he could do.
A possible plot is that Naruto is constantly bullied because of his neglected state and his unknown bloodline. As he grows, he starts to show signs of his bloodline powers, which attracts the attention of both friends and foes. His journey then becomes about controlling his powers and dealing with the past neglect of his parents while also facing the new challenges that come with his revealed bloodline.
Naruto might try to seek attention elsewhere. He could focus on his training more intently. By pouring his energy into becoming stronger, he distracts himself from the pain of parental neglect. Also, his friends could play a crucial role. Their friendship might give him the sense of family and belonging that he lacks at home.
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.
One common plot point is Naruto's search for his identity. Since he's neglected by his parents, he has to figure out who he is on his own. And with the Mokuton aspect, it often involves uncovering a hidden family connection related to Mokuton. Another is his struggle to gain power. He's determined to become strong using Mokuton to prove that he can succeed without his parents' support.
This kind of fanfiction is really exploring the darker side of family relationships. Naruto, who is already a character with a difficult past in the original story, would be even more burdened here. The neglect from his parents could make him develop some negative traits. He might become resentful, not just towards his parents but also towards his sister, at least initially. However, this could also be a setup for a great character arc where he overcomes this pain and learns to love and accept his family again.
Dark Naruto may seek solace in nature. He could go to remote places in the forest and find peace there. Over time, he might start to understand that his parents' neglect doesn't define him. He could then use his experiences to help other neglected or outcast individuals, turning his pain into a positive force for change.
The neglect from his parents in the fanfiction would deeply impact Naruto. He would probably be constantly seeking validation. This could drive him to work even harder to prove himself. His sense of self - worth would be very low initially. For example, he might be overly eager to please others in the village. However, as the story progresses, his experiences could lead to a newfound confidence and a more independent identity.
One possible story could be that Naruto discovers his unique bloodline abilities later in life and realizes that his parents' neglect was partly due to fearing his power. He then has to come to terms with this and learn to control his abilities on his own.