Anathem is probably Stephenson's best novel, and I say that as a huge fan of Cryptonomicon and Snow Crash.
I've actually found his last few novels lacking, still struggling to finish The Rise and Fall of D.O.D.O. and REAMDE. I do wish he'd stop trying to reverse-engineer RPG settings and got back to his post-cyberpunk roots.
REAMDE - don't take it seriously. The author basically just took a vacation and wrote a mindlessly fun action book. If you read it as such, it's pretty good. It's definitely written from a Western perspective, but it does have some pretty astute insights about East European mentalities and culture (I say this as someone straddling the fence between West and East culturally).
DODO is not pure Stephenson. The personality of the other writer (Nicole Galland) quite clearly changes the atmosphere. It's the first NS book where characters' emotions are actually given some attention, and the first where female characters are described from a first-person perspective (in a way that's convincing).
Funnily enough, one of my big gripes with REAMDE so far has been that Neal doesn't seem to get the Russian mentality at all. I'm not familiar enough with the Hungarian culture to judge Csongor, tho.
I love the Baroque Trilogy. It's such a different universe than his other work, and I'm a history buff so it's fascinating to read and try to figure out what is accurate, and what is his imagination.
Don't fear. The inertia from all the over the top action sequences where the reading marker drops through the stack of pages like through vacuum keeps you going through the heavier parts in no time.
Ps: Anathem > Seveneves, unless you ignore the last third. Stephenson is usually weak at the end, when all the pieces are put in place and there is no room left for brilliant tangents. Anathem suffered surprisingly little, Seveneves more than usual.
I think the issue I had with the last "section" of Seveneves was it felt more like a prologue. The pacing was entirely different. I didn't hate it or anything, but going from the previous two parts to the last one was jolting.
I'm really not sure how I feel about Quicksilver. I read it when it came out, and I remember loving it, but when the second book arrived I thought "dang, I don't remember what was happening, I should reread Quicksilver first," and suddenly realized that I really, really don't want to do that ever. I suspect that my conscious mind is only remembering the thrilling action bits, but my subconscious remembers the miles of slog in between and cringes away.
Come to think, I have the same issue with Snow Crash and Heinlein's Starship Troopers. I remember both of them as nonstop action thrillrides and suppress the endless bloviating over linguistics and ethics, respectively.
I had the opposite experience—the first time I read it, I barely made it through. The second time, before reading The Confusion, I re-read it, and fell in love with it. It gets better each time I read it.
I try to re-read the trilogy every couple of years since it's so deeply constructed. Plus the main characters are fascinating. Life is short, bump this to the top of your queue!
I made the conscious decision to just skip any plot lines where I wasn't interested. I left over half the writing on the shelf, but I think I enjoyed it more than most people who've read the whole thing.
I started in Cryptonomicon, I just doesn't catch me, I'm about 20% in but nothing happens. I like descriptive, setting an atmosphere, but Stephenson goes to far I feel. The world is different ok, fun, but it just moves so slowly. Shaftoe goes everywhere and nowhere, I get it, he saw some dragon, yes third time you mention it... I put it away. Perhaps I'll pick it up later.
