Disclaimer: I hadn't played through KS again in two years, so some of the below is reliant on foggy recollection and might not reflect the full extent of the canon source material. I also cannot claim that anything you are about to read hasn't been said by someone else elsewhere, so if you're here for an 'original' insight, prepare to be greatly disappointed.
First, some personal opinions on some of the notable dramatia personae:
Emi
I found her "never look back" attitude to life to be inspiring, as she seems to never let anything negative get to her; her cheek (tongue-in-cheek, I mean), boundless energy and concern for Hisao's well-being (even going out of her way to help with Hisao's eating habits) also helped.
On the other hand, the revelation that her father's death had impacted greatly on her life and may have been eating away at her (just my interpretation, folks) certainly put the above in a new light and made me question whether her attitude and quirks were always there in her life or were partly brought about by the above. Yet, I identified with her in this way, having lost a close family member nearly seven years ago, As my father told me only just a week ago, you can try and move on, but when something like this hits you, you can never 'get over it' - no-one should EVER say that to anyone.
Rin
I found Rin's story to be a bit of a train-wrecking bender to try and untangle during her route. Like Hisao, I often found myself scratching my head as the both of us tried to work out what made this artfully-gifted, yet sometimes 'off-the-wall' girl tick. Eventually, Hisao (and by extension, myself) came to the same conclusion - you don't NEED to get inside a girl's head and get to know them fully in order to love them for what they were. Granted, this is an aesop that is also prevalent in the other routes, but I felt Rin's dealt with it the most prominently.
On the other hand, I found myself somewhat horrified regarding how far she pushed herself - mentally as well as physically - once she begins her short-lived 'career' in the gallery. A certain incident in an atelier at the odd hours of the night, her brief experiment with smoking and her breakdown in the route's penultimate chapter - there were times when I wanted to shake my screen and plead, "For heaven's sake, STOP!".
And that 'neutral' end-scene in the fog-laced streets, knowing the implications that may or may not affect her down the trial of the years ahead ...
Whoever said that Rin's route was one of the 'darker' ones within KS certainly wasn't lying!
Shizune
As someone may have pointed out earlier in the thread, there might be girls (or rather, personality traits emulated by the cast's heroines) with whom you'd click and others with whom you'd don't. Shizune was one of those who didn't 'click' with me as much as some of the others.
Maybe I might have been affected by initial impressions outside of her route, but I found her business-like passive-aggressiveness overbearing at times. I could easily see why half of the old Student Council all but mutinied and jumped ship; whether it was because the old Council didn't like the way she ran things or whether she ran the Council into the ground under the weight of red-tape, though, is a debate for another time.
On the other hand, her route gave the character some much-needed fleshing out and I was able to move on beyond first impressions to see what really drove her. It allowed me to see the person underneath the facade of her position. The occasionally tense interactions with her father was also insightful in allowing me to see what made her tick - honestly, he can do his best for his daughter if and when he genuinely cared for her, but in general: 'what a prick'.
As for the revelations concerning Misha in this route - with or without 'doing the deed' - damn. Just ... damn.
Hanako
Hanako was the second character with whom I didn't quite 'click' with. Yet, unlike Shizune, there were parts of her character that I could identify with a bit more readily: the loss of her parents, her history of bullying in school, her tendency to 'shut down' when the stress or pressure of a situation becomes too much for her, etc.. On the other hand, the moment when she blows up at Hisao was both expected and unexpected, if that makes sense to anyone. There were signs that she resented being stereotyped and treated as someone to be 'protected' by anyone, even if they did give a genuine damn about her, but the way it all exploded in Hisao's face ... all it needed was for the ending to have been punctuated by the door being slammed in his face and I think the shock would have been completed!
In many ways, her character is the one that changes the most throughout KS' story, in spite of taking place in a shorter period of time then, say, Shizune's or Rin's. She really does 'come of age' by story's end, even in the other routes where her progress isn't fully touched on. This is something I haven't exactly seen in other VNs where auxiliary routes and the changes their featured heroines undergo are concerned.
Kenji
OK, I'm not going to lie here: there were times I honestly desired to run the poor guy through with an 18-inch bayonet. Granted, he can be hilarious (at times, I must stress) and there were memorable moments during Shizune's route where we do see the boy behind the glasses - literally, as well as figuratively. However, for the most part, a good chunk of his ranting came off to me as downright annoying rather then insightful, logic-bending or comedic. I was thus quickly turned off of the character; you can imagine my relief during one route where you can get Hisao to tune out during one of Kenji's bouts.
He probably wouldn't have been out of place on The Goon Show, come to think of it.
And now, for the character I got the most attached to, which you've well and truly worked out about a fifth of the page ago.
Lilly
OK, OK, I admit it: I was somewhat smitten by her after Hisao and Lilly's first meeting! And in a way, that's partly what her route is about - how first impressions about someone you like, know as a friend or even love deeply can be equally beneficial and, under circumstances, very damaging.
Lilly is, in my opinion, one of the most compassionate, mature and likable characters of the entirety of KS' cast, despite the hyperbole that can be concluded from this. I'm sure someone else has summed up her positive character traits better then I can, so I'll leave it at this.
On the other hand, she isn't a one-note character and her flaws stand out just as well. She feels torn between family and friends when the ugly matter of Scotland rears up, resulting in an indecisiveness and split loyalty which can nearly cost both her and Hisao everything they've built up together. In relation to this, she can 'clam up' about vital or devastating matters - though whether it's due to a fear of worrying those close to her or a belief that she should bear it on her own, I'm not sure - until (when prodded) it all comes spilling out in a flood, as demonstrated with the conversation with Hisao in Act IV and, to a lesser extent, in her good ending.
Well, that's all I have to say on this thread - I consider myself both a proud Lilquisitor and privileged to have been one of the many who have read this masterpiece of a VN. I just hope that what I have written here can help provide some insight into what made me like these characters or what I 'saw' in them.
Now, if you'll excuse me, I think I hear a church bell in Inverness ringing ...
) ... " If i would wake up in a no-man's-room and realize i'm at Yamaku now , i would go to the library , find Hanako , startle her , say sorry and keep it going " 
