I think it is very important that the foundational building blocks be established before the game even gets to teaching the Fundamental Question. Specifically, the player should get to a reasonable point where they accept the assumption that
reality exists, the basic intuitive notion that The Simple Truth attempts to convey, and the principle that things
can be learned and understood. Otherwise the userbase shrinks to those who already understand this.
I think it's also important that the game sets the expectation very early-on that the game will be fun, and preferably not disappoint. I think Kaj really understands this and already tries to consider it at every stage. And along the lines of what I said above, it should also prime the player's expectations that they will actually
learn, and that they will
actually understand what they do in the game. The effect of such expectations is well-researched in education.
It might take a lot of experimentation and prototype testing, but we need some way of figuring out what "lessons" to "teach" and in what order, and in what format the lessons should best be presented. I've mentioned Antichamber and The Sims before, and there's a lot of material on the web on making good game tutorials (or reviews of what makes a bad tutorial), but I don't know to what extent the skills this game should "teach" are different from teaching standard gameplay mechanics. It might also be that there's no relevant difference whatsoever, which would be nice and convenient.
The most amazing tutorials are those that last almost half of the game, and where the player barely even registers that there
is a tutorial. If the player think "Oh now I have to go through this tutorial sequence before I can get back to the game", then the tutorial fails this test. It's a bit of a lesser version of "Oh, now I have to answer this quiz / solve this puzzle before I can get back to my awesome fun shooter segment".
I can come up with any number of examples and things to look at on any end of the spectrum if someone wants to play some reference material (be it for tutorial quality or some other aspect).
I don't know how much of this is obvious or obscure, but I'll err on the side of assuming that everything I know about game design is obscure and arcane to most until told otherwise ;)