One common theme is growth. Both Kratos and Atreus are constantly evolving in their abilities and understanding of the world around them. Fanfictions often explore how they grow individually and as a team.
Sure. One popular fanfiction might be about their further adventures in new, uncharted lands. It could explore how Atreus grows even more in his skills and wisdom under Kratos' guidance.
It might be a story about his family, not just his own past but also about Atreus' mother. Kratos could be sharing memories of their life together, how they met, and the kind of person she was. This would give Atreus a deeper connection to his family heritage and a better understanding of his own identity.
The story Kratos told Atreus might have been about his journey to redemption and the lessons he learned along the way. Maybe it included details of the difficult choices he had to make and the consequences of his actions.
In a fanfiction, Aphrodite could see Kratos as a unique challenge. She is used to having mortals and gods alike fall for her. However, Kratos is different. He has seen too much pain and destruction. So, she decides to study him more closely. She watches his battles, his interactions with other characters. As she does this, she starts to develop a strange respect for him, and this newfound respect changes her view of him from just a target for her charm to someone worthy of her admiration in a different way.
One interesting Kratos and Atreus fanfiction could be about their adventures in a new, uncharted realm. They might encounter strange creatures and have to use their combined skills to survive. For example, a story where they come across a land filled with ice giants and have to figure out how to defeat them without freezing to death.
One common theme is the re - imagining of the mentor - apprentice relationship. Since Kratos is often seen as a mentor to Atreus in the original, when Kratos is female, it can bring a different flavor to that dynamic. For example, a female Kratos might be more empathetic in her teaching methods.