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.