Heya, I recently finished Shizune's bad ending as well, so I thought, I would post my feelings here as well, since this seems like the right spot, even tho it's been abandonded for some time
Honestly, altogether I liked Shizune's path the least and deliberately went for comforting Misha, first off, I honestly did not expect that to lead to sex right away, even if it does seem like a trend with the game (Hanako sex scene anyone? OMG, serously Hisao, girls kisses or whatever and you jump her bones instantly). And secondly at that point, like throughout the whole story pretty much, I was way more interested in Misha. At first I also actually thought that the "big issue" was that their friendship was breaking because Misha had feelings for Hisao as well and felt like a bad friend for that.
In general, I have to admit I simply did not get this route, it seemed like everything was ok (not normal, just not totally wrong yet) throughout the whole thing and than suddenly you had sex with Misha and that made things go bad, even tho that itself was never the problem.
I probably watch too much simple american comedies, so that I need to be spoon-fed the actual issue of the story, but aside for Shizune having a stick up her butt and being weird about it, I did not notice any conflict whatsoever.
For me the main problem was Shizune herself. At first i was very intrigued by her, I actually did not at all care for Misha or her avatar (strange that it ended up the other way around in the end) and liked Shizune for being proactive and interested in helping you, most people enjoy being a center of someone's attention and being the roleplayer I am, I enjoyed it and liked Shizune for it. Even her competitive side was endearing at the start and in general, first act and most of second act was just fine.
When it went wrong for me was the holiday at Shizune's house, before that I have ignored that even tho they officialy started their relationship, they have not even kissed, but when the holiday came i suddenly realized there was no relationship to speak of. To my knowledge nobody knew about it, it was never admited anywhere and Shizune even introduced you as friend at her household, if that is not a slap in the face, than I do not know what is, sure they dated only a while, but why take him if you don't want to get into that ... She ends up spending most of her time with Misha, which in itself is not bad, but not knowing that Misha likes her, makes her seem that she is just ignoring you, and I still belive that for some part she was, she just is not a lovy-dovy person, I get that, but why she would not invite you to come with at least, I do not understand. Than the weird sex scene, I mean cmon, if this VN is supposed to show that disabled people are just people, why are they all behaving like weirdos, even if it's completely unnecessary. I get that she wanted to "quiet him down", but damn, what kind of a first sex is that, without any foreplay or even kissing first, and than she goes on ignoring him. Leaving Hisao with her jerk of a father (what a douche) and never even apologizing or standing up for him against her father (again, I try to understand, Japanese customs and stuff prohibit her from speaking against him openly and such, but he was the first one to go against every expected curtesy from a host).
It was at this point where I was very much pissed at her and at Hisao for being ok with this, he thought it weird that she doesnt speak with him but never brought it up... I mean HOW?! How do you not?! After that just happened... While in other routes Hisao is a jerk or a stupid person, I could at least try and see things from his point of view (for example I actually agreed with him in Rin's route, no matter how much I like her, I was just as confused as him and felt his actions justified to some extent). But here I just didnt get it, why exactly where they dating again? Why exactly he liked her? Because she was competitive and hard working in the student councel...? Is that enough?
And than the "big issue" arc came and it turned out to be issue mostly between her and Misha. There was no big issue and the issues that I had with their relationship and her treatment of just about everything and everybody was never brought up or discussed (ok at the end she admits that she may have been a bad girlfriend, damn right)
So hell yea, I'd like to think that Misha came to Hisao because she kinda liked him as well and some of their conversations later on made me thing it's actually possible as well, even they would never admit it or talk about it, since they both felt ashamed (I read pretty much all posts here, some of them clarified some things and were helpful, thanks ^^) But he was already with Shizune and instead of thinking about why he did it (even tho he really did not have to, you can comfort people without immediately taking their clothes off Hisao) Same went for Misha, she was thinking about how guilty she was and how much this would hurt Shizune instead of why she did it. I choose to belive it was because she was confused and sad and a little bit angry, but also because she liked Hisao, not because she wanted to be closer to Shizune in some twisted way.
And than Misha ignore Shizune and than Shizune ignores Misha, for reasons that are still beyond me. Misha is in love with her and probably feels like a third weel and that is why these feelings are resurfacing, with Hisao around, but they were at a stalemate for years and I just honestly don't understand why is this a thing, this must have been discussed between the two of them at least on one occasion.
So the wheel of ignoring continues, to that add the infidelity which in my eyes was caused by Shizune, just as much as Hisao and Misha and everything ends up unresolved and at a dead spot, with everyone feeling guilty, sad, unsure about their ways and stuff.
And when the bad ending came I was just thinking, whether she knows or not, this relationship was just awful and deserves to end, they were in a platonic relationship for the most part anyways and why that is is never said, not really (yea i know Shizune atracts people and than pushes them away, why tho?)
There was never any real conflict to be had if they just spoke to each other, actually confronted things together and sorted them out, but that was never possible mostly of because how Shizune simply is. She always has her way, disregarding people's feelings a lot, and is way too focused on the student council projects, it actually made me mad, how often that was simply all that was happening.
Like I said, I probably didn't get this route at all, but except for Hisao cheating on Shizune (which is of course despicable) and him being placant the whole time, even through things where any normal person would open their mouth, it was all on Shizune. Her inability to adapt and explain stuff, her always keeping Misha around even if it must be painful for her. Her simply being a crapy friend and girlfriend.
Generally I dislike Shizune, sorry to those who like her ^^ feel free to enlighten me.