On a more personal level, they could face internal guilt. As Naruto grows up and achieves great things on his own despite their neglect, Minato and Kushina may realize what they've missed out on. This realization could cause them a great deal of internal turmoil and regret for not being there for their son when he needed them.
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 this type of fanfiction, their relationship could be developed through Naruto finding a way to communicate with Kushina's spirit. Through this communication, Kushina can share her experiences of being neglected with Naruto. Naruto, in turn, can tell her about his own struggles. This exchange of experiences can create a stronger bond between them, and Naruto can then strive to make sure that no one else in the village feels the neglect that they did.
A plot could involve Naruto finding a hidden diary of Kushina's where she wrote about her feelings of being neglected. This could lead to Naruto having a new understanding of his mother and also make him question the way the village has treated him. Or perhaps in a different scenario, both Naruto and Kushina are sent to an alternate dimension where they are both neglected, and they have to rely on each other to find their way back while also dealing with their emotional baggage.
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.
One possible reason could be for Naruto's protection. Maybe she thought by banishing him from a certain place or situation, she could keep him away from a hidden danger that she knew about. For example, there might be a powerful enemy targeting Naruto specifically, and she believed that by making him leave, he would be harder to find.
Another aspect could be that the fanfiction delves into how Kushina's presence affects Naruto's relationships with others. For instance, his relationship with Sasuke could be different. With a strong maternal figure in his life, Naruto might be more stable emotionally and be able to approach Sasuke in a more understanding way, which could potentially change the whole dynamic of their rivalry and friendship.
One possible reason could be some sort of dark influence or curse that makes her lose her maternal instincts. Maybe a powerful enemy targets her and in order to protect Naruto from further danger related to her, she feels forced to abandon him. Another reason might be that she is made to believe false information about Naruto, such as that he will bring great disaster to the village in the future.
One possible reason could be a mission. In many Naruto - related stories, missions often take characters away from their families. Naruto might have received a highly important and dangerous mission that requires him to be away from Kushina for a long time.
He could learn powerful sealing techniques. Kushina was known for her sealing skills, and she could pass them on to Naruto. This would give Naruto an advantage in battles and also in containing the Nine - Tails' power.