The pairing always felt more about ideological inheritance than romance to me. Luffy carries Roger's will, Yamato carries Oden's—it's a bond built on legacy and freedom, not glances across a deck. So much fanfiction gets that wrong, bending them into a generic shoujo dynamic. The good stuff latches onto their shared obsession with liberation; Yamato wants to be free from Kaido and Wano's borders, Luffy IS freedom. I've seen a few fics that nail the almost mythical quality, where Yamato sees Luffy not just as a person but as the embodiment of the dawn he waited for. Those can be haunting.
Weirdly, the gender stuff adds another layer. Yamato identifies as Oden, a man, but the fandom and official material are... messy there. Some fics ignore it, which feels disrespectful. Others make it central, exploring what it means for Luffy, who famously doesn't care about titles or gender, to just accept Yamato as Yamato. That's where the relationship sings—in that utter, simple recognition Luffy offers, which is something Yamato never got from Kaido.