Have you ever read Hal Duncan's Book of All Hours: Vellum. It has more of a mix of mythology and science, but it is very densely layered in a similar concept to Stephenson although the effect is somewhat different. Early on in the book, it reminded me slightly of Snow Crash, but that impression fades fast. Note that there's a second volume to it called Ink, and the first book ends a bit abruptly for some people's taste (though I didn't see it being an issue, myself).
I finished the first volume of the Baroque Cycle (it was the first book I bought for my Kindle!) and enjoyed it a lot, but it took me a long time to read, longer than his other works.
I personally do not recommend His Dark Materials; my wife didn't like it at all, and I found it a bit shallow for my taste. It's not terrible, but if you're not someone looking to poke a stick in the eye of religion (& in a wider sense, authority figures of every kind) with a serious mad-on about the matter, I don't think you'll find it worth the time.