Overall impression? I enjoyed reading it, and I'm glad I read it, but...
The real meat on the bone here is a classic Sci Fi McGuffin, which is to say it departs from what we regard as 'real' as a central plot point. This is contrary to what Stephenson did Cryptomicon and Baroque Cycle novels, whose punch for me came from their grounding (mostly) in reality. In particular, the Baroque Cycle novels are a pretty painless introduction to the upheaval on several fronts that happened in Europe in the 17th Century. There's plenty of yarn-spinning, but it does a good job of accurately portraying the intellectual revolution in which the yarns are imbedded.
'Anathem' has a certain amount of interesting intellectual gymnastics centered on mathematics, quantum mechanics which I enjoyed as far as they went. But for a novel that is -- to perhaps oversimplify -- a cri du coeur for rationality, it is least convincing and weakest where he jumps off from what is possible in ground reality.
And the ending is so murky about What Actually Happened that I feel like I have to re-read the last 200 pages to see if it hangs together.
Now maybe this novel seems unreservedly brilliant to someone who can explain away my reservations. Or maybe I'm Missing The Point in a big way. But I don't think it measures up to the Baroque Cycle. That doesn't mean it's bad, just that there are things about it that just don't hang together for me.
If you've read it I'm interested in what you thought, and if you haven't, I recommend it. As a substantial, pleasurable read, there isn't anything else current I could recommend over it.