Like others said, Rin's very difficult to write properly. Both her way of thinking and her way of speaking are so unusual that writing her is probably a matter of instinct. Without that connection, every single line you'd have her speak would be a puzzle you had to figure out. It's hard to write a fic that way. Rin's whole point is that you can't really figure her out all that well and that you don't need to figure her out in order to be with her. Hanako, on the other hand, is fairly easy to write. Put very bluntly: she's shy, she stutters (more in fanfics than in the VN since stuttering is a useful, albeit lazy, way of showing who's speaking), she has low self-esteem and is prone to anxiety. Hanako's remarkably normal underneath that shell of hers, so it's fairly easy to emphatize with her and deduce how she thinks and how she'd react in certain situations. Unlike Rin whose leaps of logic can rival Kenji's at times.
There's probably another reason. I think a lot of epilogue fanfics are some kind of wish-fulfillment. We didn't want the VN to end, but it ended anyway and now we're fantasizing about how things would have proceeded. I'm not sure if Rin's route really tied things up nice and neatly, but at least Rin was no longer starving herself and was at peace with the way she was. Hisao still didn't really understand Rin and actually accepted the fact that he might never actually get her, but he still enjoyed her company. It's kind of a weird ending, but personally I didn't really feel like it ended prematurely. I think if you asked 10 KS fans how they thought things would go afterwards, 9 would answer "Dunno". People didn't really feel like there were immediate things that remained untold. After all, even after 10 more acts, the player might still not have come any closer to getting to know Rin better.
With Hanako, the gist of her ending was definitely that it ended prematurely. It kind of ended around the same point as Rin's...at the point where Hisao got into a relationship with his chosen girl, but unlike Rin people most likely had pretty clear-cut expectations of what comes after. Dating, lovemaking rather than merely physical sex (the fact that Hanako only had one H-scene that didn't even involve emotional intimacy didn't help) and Hanako slowly coming further out of her shell. She and Hisao didn't really completely understand each other by the time the VN ended, but they expressed the hope they would eventually. Those expectations weren't met by the VN's good end, so enter fanfiction. It's no coincidence that Hanako has the largest amount of epilogues written...her route ended at the very moment the relationship started and people were dying to see more. That's why Hanako epilogues have always been kind of popular. Most of KS' endings didn't leave a void the way Hanako's ending did and people don't like voids. Sisterhood was actually one of the many epilogues that were written. (from the top of my head I recall at least 4 others, some finished others not)