Another theme is secrecy. Since their relationship is not something that would be accepted easily in the Twilight world, they often have to keep it a secret. This can lead to a lot of drama and tension in the fanfiction. There are also themes of self - discovery. As they explore their relationship, they also discover new things about themselves, like their capacity for love and acceptance in ways they didn't expect.
Many Jacob x Edward yaoi fanfictions also deal with themes of sacrifice. They might have to sacrifice their relationships with their respective families or packs/covens for the sake of their relationship with each other. And of course, there's the overarching theme of love. How they fall in love, how they express it, and how they deal with the challenges that come their way because of it are all important aspects in these fanfictions.