One common theme might be the idea of redemption through their relationship. For example, in some fanfictions, Obito's journey towards redemption could be intertwined with his memories of Rin. Their relationship could be seen as a source of hope and a reminder of his former self. Also, the theme of sacrifice could be present, as Obito sacrificed a lot for Rin in the original story, and this could be further explored in fanfictions.
If we consider non - inappropriate interpretations, common themes could be their unrequited love. Maybe Obito's long - held feelings for Rin that were never fully expressed while she was alive.