Right, sorry if I don't read through all 35 pages of the rest of this thread, but honestly, when I try to put my head to this subject, I come to a couple quick conclusions.
First off, the obvious, she has no clear external disabilities, so she almost certainly has something internal, such as a looming major organ failure like Hisao, or something that would require constant medical attention, like some form of cancer or Leukemia or some other major illness.
When you're talking about the "clues" of Misha getting dizzy on the stairs, or being clumsy, and you are talking about some sort of major disease or organ failure, then it really does nothing to narrow it down - almost any serious malady, or the drugs that are used to treat those diseases (such as chemotherapy) or injuries can leave the person weak, anemic, or just generally uncoordinated... and that's assuming Misha isn't already klutzy just by nature. It's not like Yuuko needs a disease to make her bump her head or be clumsy.
There were also some points I saw in things like that Neuman video, where she's foreign, and knowing sign language, but again, there is no proof that it is related to any disease in particular, although having at least some experience with deafness because of knowing at least some sign language is the most reasonable and telling piece of evidence I have heard.
Hence, I draw my conclusion that if you "follow the clues", you can basically give Misha almost any chronic disease you want, and it would fit the criteria, which reminds me of something I remember reading on a blog called Less Wrong, talking about scientific theories: That a theory's strength doesn't lie in what it allows, but in what it allows, because if you make a hypothesis that allows any possible outcome to happen without breaking the hypothesis, then you have effectively zero knowledge.
Rather, I think that it's better to look at this from the perspective of how the devs want to use Misha in the plot: She isn't a pursuable character, and functionally exists as a prop in the plot, something that negates Shizune's disability so that you can have conversations with Shizune during Act 1. Because of this, I think that there's basically two ways to go with Misha:
First, Misha is nothing more than comic relief. She has something that is functionally unimportant to the plot, and in which case, I kind of expect her to have had cancer or leukemia or something in the past, had chemotherapy to treat it before Hisao ever came to the school, but has already mostly recovered, and is just a little unstable and wobbly as a lingering effect. She's basically ready to go out into the regular world again and live a fairly healthy life, but rather than kick her out to go to a normal school, they let her stay to finish out the rest of her high school years as a Yamaku student, since she got along with the others there. (I also like to think that Misha's actually got really short hair or is just bald, and her "pink drill hair" is actually a wig, and she just bought the most outrageous one in the shop. You'll actually see her at the end of the game, and she'll have short brown hair.)
As a "first and a half", it's possible that she can mostly be comic relief, but have some dramatic backstory behind it. She could have had some sort of very protracted battle with illness, the sort which had left her in the hospital since she was basically a toddler, and she has essentially never been out of a hospital until she came to Yamaku, when she had finally started to really overcome her illness, and she's basically finally able to actually go out and about. In this case, her extreme energy, lack of volume control, and clumsiness are all explained by her being too sick in the past to be able to talk properly, being bedridden for most of her life, and not having any friends or people she could converse with, besides maybe her parents or nurses, and now that she actually has that option, "OHMYGOD, HI HI HI! I NEVER MET YOU BEFORE, HEY, LET'S BE FRIENDS, OK? I NEVER HAD FRIENDS BEFORE, OHMYGOD, WHY ARE WE JUST STANDING HERE, LETS GO DO SOMETHING! WAAHAHAHHA!" If she could actually speak, it's possible that she was simply a wardmate with someone who was deaf, and as such, learned sign language simply by being some other deaf girl's friend, because she was stuck in a bed with nobody else to "talk" to for years on end.
Either way, Misha basically is fine and getting better, and can generally just keep playing the role that she currently plays in the game, although if you go the Shizune route, and Hisao learns sign language well enough to converse directly with Shizune, then her role basically gets faded out, and she becomes less important as a character, if more her own person, because she isn't just Shizune's right hand anymore.
Secondly, however, Misha can be an instrument for injecting some extra drama. She can still have basically anything, but the main point is that she's getting worse. For an ironic twist, I think it might even be amusing if Misha has Arrhythmia, and that's the reason why Shizune and Misha are the only ones, aside from Hanako, you can't just outright say you have arrhythmia to in Act 1. Anyway, the point is, she basically goes down at some point later on, (not necessarily dead, but possibly put back in a hospital ward) after Hisao has some chance to learn a little sign language, and suddenly, Shizune's prop to communicate with everyone else is gone, and she's left almost totally alone again, except, of course, for Hisao, who she would have much more reason to depend upon for daily life without Misha around. Insert dramatic love story here.
Anyway, it would also explain the whole, "she doesn't get a part to play, because she's actually a vampire, and dies, but gets to be part of all the fighting games, isn't it sad, Micchan?" thing fairly neatly.
There is, however, a third option... "WAAAHAHAHA! You have done well to get this far, Hicchan, but now you know too much! That's right, *I* am the final boss, and empress of the New Feminist Empire! WAHAHAHA! One year ago, I set my plans into motion by draining Kenji of all his manly superpowers, taking them all for myself! Now, when I have yours, I will be INVINCIBLE!" *Commence Misha rapes Hisao scene.* After which, clearly, Lilly tries to stop Misha, but then gets caught up in a gun kata battle with Shizune on the burning rooftops of a major industrial plant that they were near for no reason because it was finally time to decide who would inherit their secret ninja school, and the day is only saved when Rin learns the true meaning of her foot chopsticks, and uses them to pilot her Super Robot, which gives Hanako the courage to finally use her witch magic openly to save the day. Oh, right, and Emi was a time traveler, but that's not really important.