The father-daughter thing between them is such a weirdly fertile ground for fic. Canon gives you this massive, brutal distance—Jotaro's basically a ghost in Jolyne's life, which is tragic and frustrating but also creates this huge space for invention. Writers can fill it with anything from bitter, post-prison reconciliation fics where they're both too angry to speak, to AU scenarios where he actually raised her and you get to see a softer side of him that he'd never show anyone else. It's less about romance for me (though some fics go there, which is its whole other can of worms) and more about exploring legacy and inherited pain. How much of Jolyne's stubbornness is his? Does he see himself in her recklessness and hate it, or admire it? Stories where they're forced to work together on some non-Stand threat really dig into that. They're both so prideful and bad at talking, so the emotional payoff is always delayed and messy. I've read a few where Jolyne ends up saving him, reversing their roles completely, and those hit different.
A lot of the more interesting takes I've seen actually sidestep the prison timeline altogether. There's this whole subgenre of 'Jotaro actually comes back' AUs, where he tries to be a dad after being absent for a decade. Those are rarely happy sunshine stories; they're full of missed birthdays, awkward phone calls, and Jolyne testing his limits. The dynamic isn't clean or heroic. It's two people who share blood and a terrifying destiny but have to learn how to be a family from scratch, if they even can. The Stand battles almost become a metaphor for their emotional fights.