A little lot of late to the party but I think this is an excellent post so I'll throw in my 2 cents. (Note a fair number of generic spoilers)
Hanako: I definitely agree that the trauma she suffered losing her parents, being in the burn ward and inevitably spending most of her life in the orphanage "not being picked" shaped her. I'm not sure it's fair to say that Hisao would have been less interested in her. To be perfectly honest, Hanako is a REALLY attractive girl, much more so than Iwanako in my opinion. Given it takes Hisao a LONG time to really get that Hanako just wants to be treated normally, I think were he to have an attraction he would have actually done far better with her than he does in the actual story. Or do you suppose it took a conflict and overcoming that conflict to actually make their love blossom?
Shizune: I'm not sure I agree about the deaf part limiting her communication entirely. Granted, it definitely limited how well she could communicate growing up and that lead to a level of isolation, but it seems that part of her upbringing was to be insanely competitive. One thing that they included in the pre-release that makes this very clear is that Jigoro says something along the lines of Hideki would get the business because he was a man and men are always better. Shizune would ALWAYS be second place in his mind. I think deaf contributed but that someone with her drive and motivation would always been seen as the "class rep" type that came off smug and pushed people away. If anything Misha actually softens some of the offensive things she says and she is allowed to choose her words more carefully. I can only imagine how she would be with absolutely no filter.
Emi: I don't really know about Emi. I think she likely would have remained an athlete but I doubt she would have had the drive to be the absolute best. I think her father dying and the trauma she suffered pushed her to run excessively and push her to the limits. I could see her as a similar type of person except the drive to push herself and excel.
Rin: I haven't played so I won't comment on.
Lilly: I would say the one thing that her blindness effected was her having to live in Japan when her family moved. They at least hint at the fact that her being blind and that being a "faux pas" are major motivators of keeping her hidden away at boarding school. Then again, without that catholic school girl thing going on she wouldn't be nearly as sexually repressed and might not go to town on Hisao every chance she got. :-D
Speaking of long winded... I guess I sent to town here. Awesome post! I don't know about anyone else but I always love a good KS discussion. :-D