You know, it's funny - Luffy and Reiju isn't a pairing I think about much, but I've read a few. The most obvious tension is always the family loyalty thing. Reiju's stuck with the Vinsmoke family baggage, all that cold, militaristic upbringing, and then she's drawn to Luffy who's like the complete opposite of everything she was raised to value. But honestly, that feels kinda overplayed in a lot of fics. Like, it's a conflict, sure, but it's surface-level. The more interesting ones I've seen dig into her self-image versus how he sees her.
He doesn't care about her past or her modifications, right? But she does. So you get this dynamic where she's wrestling with whether she can accept his unconditional acceptance, if that makes sense. She's waiting for the other shoe to drop, for him to realize she's 'damaged goods' from Germa, and he's just... not getting it. That internal conflict of someone who was engineered to be a weapon trying to fit into a crew that's all about freedom can be way more compelling than just 'my family bad, your crew good'.
Plus, there's the whole 'older sister to four emotionally stunted brothers' angle she has. She might feel a misplaced sense of responsibility to them, even after everything, and Luffy wouldn't understand that obligation at all. That creates a quieter, sadder kind of friction.