I'll agree that your male pictures are somehow...better. I guess it might be just a matter of experience drawing them or style or preferences... regardless. I wondered if the setting was already agreed upon?
Also, there's an ever-present problem of how to deal with the disabilities in the long run. Are they an important or even defining part of the characters? Can their influence be lessened or even nearly negated - most of all, should it be? Are the disabilities something the characters want to dispose of, and rightly so, something they've come to rely on and live with, or something that defines them?
If the disability is to be "overcame" with time, at which extent should it stop?
Regardless, here are some things I think deserve to at least be suggested/brought up:
1) How we deal with the entire "I'm going for this girl" thing? Do we lock somebody onto one path for most of the game, or quite the opposite?
2)There are basically two ways in VNs on how to obtain a good ending with a girl. One is obvious and quite correct - spend time mostly, if not only, with her. The other suggests a complex social network - you need help from others, perhaps everyone else, to win said girl. In "Flower Shop", a VN/Dating Sim/Farming Sim, there's a slightly counter-intuitive storyline progression in which to win a single girl you basically have to associate with at least three of the four main female characters and have to associate with one other character about as much as the girl you're going for (since associating with each girl increases a single stat, and each girl is attracted to a lesser degree to the stat she increases and to a greater degree to a stat another one increases).
3) Endings. Do we go with the simple, good ending, bad ending, and possibly middle/better/true ending? Or do we apply a different formula?
Personally, I think it is good to consider that a girl may have a set of endings far differing from bad-good-better. Also, we may have to consider a good as well as a bad "single" or "just friends" ending.
4) Finally, the main character's role. Basically, he either has to be part of medical staff, family of a chief member of the medical staff, or a patient himself.
If he is a patient, he needs a mental problem that both makes him disabled as far as disabilities go, but also doesn't make him unplayable.
Merlyn_LeRoy mentioned auditory hallucinations, and I think it is an excellent idea.
First of all, we are left somewhat confused as to whether the hero really thinks that way, or is something he hear utterly the by-product of said hallucinations. It is also a good way of explaining however weird acts we'd need him to undertake, plus, it makes his character more interesting and allows him to have "imaginary" friends or believe that it is someone else trying to communicate to him at times (while, in truth, it is still just his disability).
How it could develop : If we're going for the hero and heroines somewhat controlling/overcoming their disability, then initially in romantic/sexual situations the voices could spoil the mood or intimacy. The hero would eventually learn to drown them with his own thoughts or emotions for short whiles, thus allowing him to spend quality time with friends/girlfriends.
If we're going toward him growing together with his disability, then the voices could eventually "take shape" and always manifest as certain characters, rather than random, disembodied and different voices.. Whether the hero realizes that only he can associate with said characters or not is up to the writer.
Otherwise, we have to come up with something else, that could shape the gameplay but would drastically alter it. Split personalities and so would be great for a romanced girl, but not for the main hero. It technically makes the point of developing his character moot, unless one of the personalities were highly rare to surface.
I think overall paranoia or a phobia might work well. In the second case, we need to pick something that pretty much rules out the guy from open society but doesn't neccessarily hurt his development or relationships. He could be scared of men (as in males), which would justify putting him in the more female-populated parts of the facility. He could be afraid of anything related to transport or communication, which would make it hard for him to live in the open.
I'd sooner pick obsessive-compulsive than bipolar in case of the main hero. It could even lead to funny situations.
Other than that, there's a question of what justifies putting someone into the facility that will be the main area of the game. As mentioned, we should avoid Asperger or autism. I think down's syndrome and pretty much any chromosomal defect that connects to a mental disability or retardation is out of the question, with possible exception of Klinefelter's along with hermaphroditism or transgender tendencies... but I doubt being, more or less, "a trap" would attract the main character romantically or justify staying in our awesome facility.
Unless we put both hermaphroditism or Klinefelter's or anything that may cause such gender ambiguity and then slap multiple personalities onto it, with one or more of them having a gender identity disorder. That would be a challenging character to write.
As for the girls you proposed... As I mentioned before, I'd be against "rape as backstory". The behavioral change/delusional girl is pretty interesting, especially how the hero would cope with her... basically not being her nearly all of the time.
Kleptomania is an awesome idea. In case of "overcoming" said disability to a degree, the hero could help her develop a habit of quickly occupying her hands whenever she has the desire to take something, or blurting out a plea for letting her borrow the thing she is about to steal. Also, it'd justify one of the girls being pretty much average but with a twist.
I'd avoid PTSD/survivor's guilt unless we were going completely extreme and the memories of said trauma would temporarily and drastically as well as unpredictable alter the character's behavior.
As for suggesting anything, I'd go with kleptomania (which you already suggested), or alternatively, pyromania (not enough dangerous women these days). Split personality would be great to work with and provide many endings, but I feel it would require more than one writer on the whole character. The character's development could end with a downer ending, where one of the personalities decides to "off" the other one, leading to suicide, or to any of the three happy endings : one personality ultimately prevailing or the personalities accepting each other and switching between themselves more voluntarily. Yes, this is inspired by another work of fiction.
Also, sadomasochism (and in nearly ABSOLUTE avoidance of the kinky matters, mind you) instead of suicidal tendencies or schizoaffective instead of depression or bipolar would work in my books.
Long post is long, so I'm gonna finish it.
