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.
It might be due to jealousy. If Minato was getting more attention or praise in the village for his achievements while Kushina felt overlooked, that could create resentment. Say, Minato was constantly being hailed as a hero for his speed and battle tactics, and Kushina, who also had great power, felt like she was in his shadow.
The village of Konoha would also be affected. With Minato still alive, he could continue to lead the village and make different decisions. This might change the relationships between Konoha and other villages. For example, there could be more peaceful alliances as Minato is known for his diplomatic skills. Also, Kushina being alive would mean that the Uzumaki clan might have a stronger presence in the village, which could lead to new jutsu developments and a different power balance within Konoha.
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.
Well, in some fanfictions, the moment when Minato sacrifices himself to save the village while Kushina is already dead is extremely emotional. It shows his selflessness and also the love he has for the village and his family. Also, the flashbacks in some stories about their early days together, like when they trained together as young ninjas and slowly fell in love, are really sweet and emotional.
In many Naruto fanfictions where Naruto meets Kushina and Minato, it often creates a very emotional scenario. Naruto finally gets to meet his parents who he has only heard about. It could be a heart - warming reunion where they share stories, hugs, and Minato and Kushina get to see how far Naruto has come.
Perhaps in this fanfiction, Naruto turns to the darker side of the ninja world. Since he lacks the love and guidance from Minato and Kushina, he might be more easily influenced by Orochimaru or other villains. He could start to believe that power is the only way to get respect and recognition, and thus embark on a path that is different from his canon self. He might also form unexpected alliances with characters who are also outcasts in the shinobi society.
One consequence could be that Naruto becomes an outcast in a different way. In the original, he was an outcast because of the Nine - Tails, but here, it could be because of his abandonment. He might not have the same dreams of becoming Hokage. Instead, he could be more focused on survival.
At first, Naruto and Kushina might start to distance themselves from Minato. They could avoid him and not talk to him as much. As time goes on, the hatred might grow deeper. Naruto could start to oppose Minato in public or in important village matters. Kushina might also try to influence others in the village against Minato.
Minato would probably be very proud. He might notice Naruto's use of his own jutsu and be impressed by how Naruto has developed his skills. Kushina would be more emotional, maybe crying at the sight of Naruto growing up so well.
Well, it could be that they find out some 'dark secret' about Naruto. Maybe they think he has some sort of uncontrollable power within him that they fear. Or perhaps they are forced to disown him due to political pressure in the village. There could be a group of elders or powerful clans that demand it in order to protect their own interests or maintain the so - called 'balance' in the village.