Another theme is the exploration of relationships. Female Goku might have different interactions with other characters. For instance, her relationship with Vegeta could be explored in a new light, perhaps with more of an emphasis on mutual respect and a different kind of rivalry. There could also be new friendships formed with female characters that were not as prominent in the original series.
One common theme is empowerment. Since Goku is already a very powerful character, in these fanfics where she's female, it often emphasizes her strength even more, showing that gender doesn't limit her abilities.