For me, the game's elements started to work together only some time after reaching the end; in my mind. I had to realize what it was all about, first.
I would have liked it better if the game's idea would have been approached through a gradual build-up in my awareness, while playing the game, instead of coming as a surprise at the end; or rather, beginning with the end. And I believe that, by trying to make the player aware of the game's idea through the various game elements, not only would everything have worked more harmoniously, but some minor weaknesses would also have been, implicitly, avoided.
There is one category of minor weaknesses that is of particular interest in connection to the above: bits of the protagonist's attitude that could stand in contradiction to the main idea. One example is treating the friend's house as that of a stranger. Shouldn't it rather be evoking some memories, even if only vague ones? (And I'm refering to the furnishings, of course, not the books' contents.) For the case when you agree that this would have been a better choice, I add that this change would be one means of making the game's idea available during the time of playing.
If keeping the game's idea a secret is a must, then there is an alternative way to achieve cohesion, while not (gradually) sharing it: richer and more dynamic interactions, both between the protagonist and the game world, and between the protagonist and the player. As it is now, not much is happening in the game to keep the player engaged.
This is probably obvious, but I will say it, if only to avoid an abrupt ending: Without enough cohesion, the various game elements stand individually out more, and that may lead to them being appreciated only as such; instead as one game.
There was one compensating factor, at The Chrysalis: that you did not try to achieve too much for a short game, KC. And this may be off-topic, but I would like to say that I enjoyed the game for its modesty, the most.