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Lilly's route is a very good example of what happens when a KS route gets past the whole "cripple girl" issue right away. Lilly ain't shy about it, it doesn't get in the way, and her story goes on to cover what's going on in her family and social life. She's having doubts about whether she is enabling Hanako in acting almost more like a mom than a friend to her, she's got her family's expectations to worry about, and then she has to make a hard choice between Hisao and the call to return home. It's all tough stuff to work out, none of it has anything to do with her being blind, and she's all the stronger as a character for it.
Whereas with Hanako, she's completely defined by her massive complex, and there's very little to her outside of it. That one little aside she had about playing the game of "don't step on the wrong tile" was something that the fanbase latched onto hard primarily because it was one of the few aspects about Hanako's route that actually gave her something resembling a personality. It's also the reason everyone loves her bad end scene - because she finally opens up and makes it clear that she has thoughts in her head which are actually introspective. But you don't get any of that if you don't actually take the path that puts you on the bad end! Lilly's blindness was little more than an accessory to her character, whereas Hanako's personality was an accessory to her disability.
The same happened with Emi, though to a lesser extent. Yes, her real issue is with the death of her father, but she also has a massive complex about being treated like she's handicapped, which she is. It doesn't completely take over, because she always has her track and field as a hobby, and there are enough instances of her doing things that show she actually has interests outside of her handicap.
That's what I mean about the narrative butting in on opportunities to develop the characters. You hardly even notice that Rin doesn't have arms during her route, except for the fuss that other people make about it - the trouble is that she is forgetting to treat Hisao like a person with his own affections and needs in a close relationship. You hardly notice that Shizune is deaf outside of the physical limitations that imposes on her, because the focus is on how hard you're NTRing Misha. And again, Lilly gets a very strong development because very little time is wasted on pointing out how her blindness inconveniences her life. There's a limited word count for every route, and the more of that word count is spent on poo-pooing the act of white knighting for a crippled girl, the less is spent on dealing with more important, less skin-deep issues.
It's kind of like how you have to get past Shirou's white knighting in F/SN to learn that what his problem really is amounts to a massive survivor's guilt complex, and that Saber also has a hero's complex - the two of them have to overcome their own obsession with taking on all the burdens of their own and everyone else's problems in order to work together properly. There's juicy stuff under the surface that we as readers want to get to, and it's disappointing when what's on the surface winds up being all or most of what there was to it all along.