To get to the point: Yes, Anathem is disappointing.
Reading the book, it was hard for me to keep from comparing it to Snow Crash, Stephenson's breakthrough work. As far as I'm concerned, Anathem is his first real attempt at worldbuilding since then. Like the earlier book, it contains vast swathes of exposition on the central plot conceit--then a mashup of Chomsky's universal grammar and Sumerian legends, now a confusing muddle of quantum mechanics and Western philosophy. And the two have a kind of elite-vs.-the-masses viewpoint underlying their narrative, which in both cases is ambiguous if not a little disturbing. But sadly, Anathem's no Snow Crash. It's talkier, longer, duller, and far less fun to read.
Stephenson sets his story in a world called Arbre, in which the medieval system of monastaries/convents and uneducated masses has been recreated, and which has apparently persisted for thousands of years. During this time, the monks have been sacked three times by the "Saecular" nations during revolutions, and each time they've become even more spare and inwardly focused. Each convent only opens itself to the public at predetermined intervals--some every day, some every decade, and a very few only at century and millenial ends. One year, just after his group temporarily unlocks its gates at the start of the decade, a monk named Erasmas gets swept up in a complicated conspiracy when a spaceship appears above Arbre for the first time.
The setting isn't bad--it's kind of a postmodern Canticle for Leibowitz--and Erasmas is an inoffensive, if slightly bland, character to stand in for the reader. But the plot, almost 1,000 pages of it, just isn't that exciting. Worse, it's punctuated by long stretches of characters standing around explaining quantum mechanics to each other through unexciting metaphors. Like a lot of sci-fi, setting up a central idea isn't unexpected: Snow Crash did a lot of the same thing, but it also had two things going for it: first, it had two characters to switch between when the going got too tedious, and second, the intervening action was a lot more exciting. Granted, it was a tall tale and this is not. But there, if you skipped the stories about En and the Tower of Babel, you got to read about Y.T. the skateboard Kourier and Hiro the greatest swordfighter/hacker in the world. Even in the parts of the Baroque Cycle that I've read, in between treatises on 18th century commerce, there are pirates and political intrigues. Here, your reward for skipping exposition would be either a slog across the equivalent of the north pole (somehow rendered without drama) or a list of mathematically-precise maneuvers in zero-G.
But even if you dig the plot and the discussion, I've also got bones to pick with the technical aspects of the writing in Anathem's pages. For one thing, Stephenson's apparently just given up completely on writing a realistic female character (which is a shame, given how much fun Y.T. was). For another, every character in Anathem has pretty much the same voice, which is in turn pretty much the same as Stephenson's authorial voice. We saw hints of this in Cryptonomicon, which tended to blend its protagonists voice with the prose style, but it's extremely pronounced here, and the result reads in a kind of stilted, geekish monotone. If nothing else, I wonder what kind of barbarity contractions must have performed on Stephenson in the past, he shuns them so readily. The author also continues his long history of setting up liberal-arts straw men for his scientific protagonists to knock down--a tendency he's had since Zodiac, although it only became truly pronounced in Cryptonomicon, which featured a disconcertingly vicious parody of relativism and academia.
There's nothing wrong with writing concept novels. That's why we have science fiction. But great concept novels need to be thought-provoking, and Anathem isn't. After you break down the speeches and the theorizing, without spoiling anything, what you're left with just isn't terribly interesting or novel. The setting's separated communities are never really used for anything other than some deus ex machina, and their potential for commentary or satire is largely wasted. I finished the book feeling like I had myself been locked in a dusty room for too long, and was glad I could finally open the gates.