I'm not sure who Aku specifically is. Aku could be a person with a great imagination who tells all kinds of stories, like adventure stories, fairy tales or even true - life stories.
It could be someone from the Naruto universe who doesn't like Naruto's newfound fascination with Aku. For example, Danzo might see Naruto's interest in Aku as a threat to the stability of the village and try to stop Naruto from further exploring Aku - related things. So, Danzo could be the main antagonist in this case.
The character of Aku could be developed in a 'pregnant Aku in Samurai Jack fanfiction' by exploring how he interacts with the world around him differently. He may become more reclusive as he doesn't want others to see his 'weak' state. Or he could become more aggressive in trying to protect his pregnancy, which would be a new aspect of his character. Also, his relationship with his own power might change. Maybe he has to find new ways to use his magic that don't harm the unborn, which would force him to grow and adapt in ways he hasn't before.
One idea could be a crossover where Aku accidentally opens a portal to the Naruto universe. Naruto, being the curious and brave ninja he is, decides to explore Aku's world. They could start off as enemies, but gradually come to understand each other's motives and end up teaming up against a greater evil that threatens both of their worlds.
I'm not sure specifically what the'sama sama letter day story' is about as it's not a widely known common story. It could be a very personal or a story from a specific local or cultural context.
One common theme is the struggle between good and evil, as Jack represents good and Aku represents evil. Another is the concept of fate, as their battles seem pre - ordained.
I'm not sure specifically as I haven't played it in detail. But generally, a visual novel often involves a story with characters, plot development, and probably some kind of relationship exploration. 'Aku no onna' might be centered around a female character who could be associated with some sort of 'aku' which might mean 'evil' or 'dark' in Japanese, so perhaps it's about her story in a dark or complex situation.