I'm pretty late to the party, glad to see there's still some discussion going on.
I do not think Shizune's route is bad, even though I used to. However, since it was the route I played last, it kept nagging me to make sense of it, and now I say Shizune's route, similarly to Rin's, requires you to think and pay careful attention to things, although in a very different way compared to what was going on with Rin.
A common theme in many of the KS stories is distance; the distance between Hisao and his love interest, or the distance between said love interest and people in general. In most cases, this "wall" is roughly composed of a single layer, which Hisao needs to get through (with Emi and perhaps Lilly) or simply has to accept its existence (with Rin and even Hanako to a lesser extent). With Shizune, it's a lot more complicated: some walls crumble, others remain, and unlike in the other routes Hisao does not really comment on this. (More about this later.) It's up to the readers to notice such facts, and those who don't might make the same mistake I did and write the story off as shallow.
The first obvious "wall" is simple communication. I have to admit: I hated Shizune in Act 1. She came off as aggressive, unfair and pompous. When I went for her route, I tried desperately to get around having to side with her during the argument with Lilly, because it just seemed so unfair. (No such luck, of course.) Hisao might have been falling in love with her (a little) as early as during the festival, but I sure wasn't. All the bigger was my shock, though, when Hisao started learning the sign language and the two of them began to communicate directly - it was like I was seeing a completely different person. Her attitude suddenly began to make sense. I found myself growing to like her, despite her obvious faults and my earlier distaste. Naturally, this was no simple coincidence - Shizune herself comments later on how the fact that she can only talk through an interpreter most of the time distances her from others.
This first "wall"is rather easy though. The second I did not really grasp during my first playthrough at all. What does Shizune think about romance? Just how many boyfriends did she have before Hisao? My rough estimate: none. During much of Act 3 and 4, she and Hisao try to determine, now that they're dating, just what the heck are they supposed to do with it. Actually, Rin faces a similar problem in her own route, only she vocalizes her concern - Shizune, on the other hand, doesn't. She simply remains distant, or when she gets fed up with that, tries to move forward in awkward ways, such as that "tied-to-a-chair" scene during the visit to her family. And of course, she then recoils because she notices how, well, awkward the whole thing was. Shizune being who she is, making this soul-searching a group effort with Hisao is out of the question, which is why their relationship fails to normalize until the end of Act 4 (in the good ending path); mind you, it happens right after she lets Hisao take the lead in patching things up with Misha, showcasing her character development.
There's a third "wall" in their relationship, however, which I believe stays in place until the very end. I think someone described this earlier in the thread as Hisao and Shizune being "intellectual lovers". Even at the best of times, when Shizune is not avoiding Hisao, heck, even right after making love in the student council room, their interaction feels slightly... "distant". There's no hand-holding, no stolen kisses or anything of the sort. This is, first of all, a physical limitation, since they have to keep each other in view with their hands free to communicate, which can make even romantic rooftop lunches uncomfortably quiet - but there's also more to it than that. Simply put, some people do not convey their love through frequent physical contact. Some would want to hug every person they come across, others shy away from such activity in general. Shizune is apparently the latter type. I would also wager that the second wall crumbled a bit too late for them: by the time they could get more "lovey-dovey", graduation is already here; it's telling that Hisao tells her "I love you" for what I believe is the first time in the very last scene.
What makes all this stuff much harder to spot than normal is how different Hisao's narration feels compared to other routes. Usually, when there's a problem, he brings it up. If Emi's not letting him close, he'll have internal monologues fuming about it. This time, however, he acts almost like an unreliable narrator in many ways. Why? Well, I think it's because he's busy. No, really.
Each of the girls have their own "strategy" or trait to pull Hisao out of his initial depression; for Shizune, it means making him busy enough that he'll simply lack the time to mope. (This is an oversimplification, but bear with me.) It works surprisingly well, too, but as a side-effect, it makes serious problems that would be better off discussed fall between the cracks of time, err, I mean the latest student council meeting - or whatever Shizune is making them do at that moment. This is the most obvious after the visit to her family: Hisao wants to talk to her about what happened there, but never gets the chance, and by the time the whole misery with Misha starts he actually
forgets about it. Since Hisao is our narrator and sole source of information, if he forgets about bringing up issues, chances are the readers might forget about them too if they're not careful. Whether this is a bad decision from the script writer is up to personal taste, I suppose, but once you know what to watch out for, I feel it can get rather interesting, since this trait leaves Shizune's route much more open to interpretation compared to others.