Well, a common theme is the exploration of a forbidden love. Since it's a gay relationship in a context where it might not be fully accepted, there's that sense of secrecy and the thrill of breaking the norms. Also, there's the theme of loyalty. Raphael is usually depicted as extremely loyal to the reader, and vice versa. Their bond is unbreakable in the face of difficulties. And of course, the theme of personal growth. Both Raphael and the reader grow as individuals because of their relationship.
The themes in 'gay raphael x reader fanfic' often include emotional vulnerability. Raphael, who might be seen as strong and stoic, shows his softer side to the reader. There's also the theme of mutual understanding. They understand each other on a deep level that others may not. Additionally, the theme of redemption can sometimes be present. If Raphael has a past that he's not proud of, the reader helps him find redemption and a new path in life, all while their relationship blossoms.