Neal Stephenson has gotten frustrated by the prevalent idea that "Stephenson can't write endings," because he feels that it has become such an idee fixe that people will find something wrong with his endings no matter what. I think he is being unfair to his critics. To be sure, he has made serious attempts to write more traditional codas to his books, moving away from having events just speed up and spin out of control so as to end the book in a singularity.
But what people are, I think, upset about is not so much that the ending is bad as that it happens when it does, that is, before all the ends are tied up. We have come to expect of novels, and speculative fiction novels in particular, that (in the words of W.F. Hermans) not a sparrow falls or it has some significance. Note that this is not at all true in the real world. I do things all the time that have no relation to anything later in my life; I start projects I never finish, not because they become irrelevant but because I forget; I meet people that I never see again; and so on. But I am not a character in a novel. In Anathem, the main character's girlfriend is separated from him, starts a relationship with some a good friend of the main character's, and later becomes involved with the main character again. There is much tension over this between the main character and the other boyfriend, but we never find out before the book ends what happens to this tension. And that is simply not allowed by the Rules of The Game, where "The Game" is the game of novel writing.
Stephenson might retort tha gossip is immaterial to the point of speculative fiction. Speculative fiction is not about psychology but about sociology, not about character development but about history and ideas. A "good yarn" is important, but from the way Stephenson frames his apology for yarn spinning, you get the idea that it is mostly sugar to make the medicine go down. Rounded characters are still appreciated, but mainly because they help paint a more vivid picture of the systemic story. And the systemic story is wrapped up, or at least left hanging from a plausible cliff: peace is established with the aliens, and the strict separation of avout and saecular, having been found wanting in times of exogenous crisis, comes up for grabs.
I can live with that, but I guess it is fair to say that books like Anathem aren't really novels in the modern sense. Which is fine. Anathem is interesting and enjoyable and stands firmly within the epic tradition, which is far older than the novel, for what that's worth.