As a side comment before I begin, I will note that, if memory serves, A22 was one of the few Americans in 4LS. I'm fairly certain that Hivemind is American, Suriko and Crud are Australian, and Aura is Finnish (to account for the writers). Assuming the Japanese cultural references were intentional (and I can't imagine why not), it certainly implies that he did his homework (and potentially lends credence to reader interpretations that account for deaf culture as well).
As I've noted before, I didn't like Shizune's route at first. I enjoyed the story, but there were bits and pieces that didn't seem right, and the ending also felt a little off. It was one of the last routes I played, so I had an interesting set of expectations as I approached her route - in the context of the other routes, she's a bit stern and by the book, also very demanding; but she shows hints of surprising kindness and attention toward others.
Shizune's route is also one of the few which I've taken the luxury to re-play (and went over it with a fine-toothed comb). The second time through, a lot of confusing and seemingly inconsistent bits from the first run fell into place, and it struck me as a much more compelling and interesting narrative.
But, overall, I'd say the phenomenon is almost to be expected.
As I
stated elsewhere, art is directed to challenge the audience (engage the intellect) or to entertain the audience (engage the emotions). Needless to say, most works of art perform a little of each role.
To expand on the terms "challenge" and "entertain," I'd say the following: The "challenge" presents an idea, concept, worldview, etc., and demands that the reader take hold of the proposition, wrestle with it, and come to a personal decision on what it means, and the truth of the proposition. The "entertain" evokes some sort of emotional response, be it happiness, sadness, anger, laughter, etc. A passive audience can be entertained, but you need an active audience in order to challenge them.
If I were to assign values of 1-5 to the routes' tendency to challenge the audience and to entertain the audience (in rough relation to each other), I'd give the following (respective) ratios:
Shizune - 5:2
Lilly - 1:4
Hanako - 2:5
Emi - 3:3
Rin - 4:4
Kenji - 1:1
This is not intended to slight any particular route, and a truly fair analysis would be better suited to rate these values on a scene-by-scene basis. It will likely also reveal my prejudices, but you can't really eliminate those - it's best to acknowledge them and calibrate your interpretations accordingly.
My biggest criticism of Lilly and Hanako's routes is that they have a tendency to tell you what to think - to conduct the majority of the interpretation for the reader. This allows for a greater focus on cultivating an emotional response. However, as I noted in that previously-referenced post, I subscribe to Maslow's hierarchy of needs as a yardstick to evaluate art. So I consider those routes to be weaker and less meritorious than the other routes.
Emi's route is kind of middle of the road - it isn't exceptionally challenging to see what's going on and to figure out the meaning of things being said and done, but it isn't handed to you on a silver platter, either. Feels are strong in places, and it's pretty consistently entertaining, but there isn't really much of a "huge impact" scene to compare to those of the other routes.
Rin's is described as a rollercoaster, and justifiably so. Very few people claim to truly understand Rin, and those that do have extremely conflicting interpretations. The vast majority of scenes are drenched in confusion, helplessness, and desperation.
And then we have Shizune's route. A few fun bits here and there, some cute scenes, the massive hammer that is the Mishabomb, and then a mountain of implications, subtle "blink and you'll miss them" expressions, cultural references, and to top it all off, a notoriously reclusive author who withholds even the barest hint of how he expects readers to engage it. And, though I have no intention of touching on it in any detail, it is the elephant in the room that, whatever such an artifact may mean, there exists a leaked draft of a dramatically different route.
In short, unlike the other routes (with the possible exception of Rin), there's no easy answer. The biggest questions of Lilly, Hanako, and Emi's respective routes can be satisfactorily answered with little more than a paragraph of exposition/interpretation (even if people are capable of going into much greater detail). For Shizune and Rin, you would need, at the very least, an extensive essay to really unpack what's going on in those routes to any degree that would do them justice. And people tend to like Rin's route more than Shizune's because of the significantly greater focus on the entertainment/feels side of the equation. Hell, the conclusion of Rin's route is pretty much "I may not understand [Rin], but that doesn't mean I can't like/love [her]."
Anyway, TL;DR - Lilly is Worst Girl, Misha is Best Girl (but Shizune's near the top).