I can think of a couple Visual novels that feature one or more major characters with disabilities, but they're both strictly het.
First is the always fantastic and highly regarded Katawa Shoujo in which all the love interests (and nearly every other character, actually) have a disability of some sort. It's free, lengthy, and astonishingly high quality considering what its background is. (Definitely take a moment to read about the devs' story if you're interested.) Katawa Shoujo was one of my first VN's and remains one of my very favorites to this day.
Second is If My Heart had Wings, which is on steam for I think $40, though price may have dropped since launch. There is one love interest (out of 4 or so?) with a disability that is a significant part of her character. This one's a long read, probably 20-30 hours depending on read speed. There's a fan re-translation and content restoration patch, though it's been a long time so I don't think I'd be any help finding or installing it. Check the community hub for it on steam and there might be a topic or guide on it.
Again these are both 100% het, so if that's something you absolutely can't stand that they simply won't be worth playing for you. If you're ok with it though, Katawa Shoujo is one of my #1 VN recommendations.
edit: oops. The OP is from nearly a year ago. Well... uh, if anyone else wants recommendations on not-yuri VN's... there it is. >.>
last edited at Feb 21, 2018 10:56PM