The fundamental subject-matter of literature is difficult loves: problems that matter deeply but are insoluble. By this standard, Bee is the most literary CYOA that I've encountered. A coming-of-age story about impossible parents, limited means and awkward emergence from isolation, it put me a little in mind of I Capture the Castle (which Emily tells me she hasn't read).
Rather than being structured around a strict linear tree like the bulk of stateless CYOA, Varytale encourages modular design more akin to RPG gamebooks or Echo Bazaar style browser-adventure-RPG games. Bee is structured around the passage of the year, with different events becoming available at different seasons; age, the state of your stats, and previous events also determine which options are available. A number of sections can be repeated with variations, but (more so than its antecedent Echo Bazaar) these are things whose repetition makes sense as narrative and as reality: chores, seasonal religious festivals. The fragmentary nature of Varytale stories is very well-suited to the retrospective style, with its assembled incidents of memory.
It should scarcely need repeating by this point, but Emily writes consistently sharp, telling prose. The story would not work without it.
One of the game's strongest points is how successfully it evokes the particular intensity of the aesthetic sense emerging in adolescence, the discovery of a transformative power, burning in isolation, standing out sharply against the world of drab concerns and tired formulas. The most prominent parts of this involve the protagonist mapping out for her own feelings about Christian ritual and the English language, but also in the seasons, in the contemplation of an emotion, in the elusive moments of family happiness. It's a story about learning to appreciate things deeply, and how to negotiate for a better deal, and reconciling the two. It's about the realisation that you're smarter than your parents. Like much of Emily's work, it's about the pathos of limitations, about lofty ambitions that will inevitably be diminished -- you're told from the outset that you will not win Nationals. (Despite the competitive framing, and in line with the Varytale ethos, this is only slightly game-like; character stats are tracked loosely, and while not every node can be found in a single playthrough, there is not really any challenge per se.)
It's also about an interweaving of shame and bristly pride; at its most documentary, Bee becomes something of an account of the culture and experience of homeschooled children. It's neither an attack nor an apology, though it has definite elements of both; it paints a more nuanced picture of homeschooling than is usual from either its advocates or mainstream critics. One obvious effect is that the protagonist has no friends in the normal sense: the listing of known characters makes a distinction between family (too basic to list) and Acquaintances, an uncomfortable and lukewarm category that's confirmed by the text. (Of course, much of this is because the protagonist's intellectual development is far in advance of everything else; it's easy to think of her as being considerably older than she is. For a while I had the vague sense that the story dealt so slightly with sex and romance because she was from a repressed religious family; but once I actually articulated the thought, I realised it didn't hold up.)
(As a technical note, I first played this when play was restricted by Story Points, Varytale's equivalent of the Echo Bazaar candle. Bee is, at present, no longer thus restricted. Generally speaking I loathe the candle system; it's horribly anti-player. But I'll admit that its artificial choke on pacing does affect how one reads, and offset the distinctly CYOA-ish temptation to hurry through the text and to get to options.)