I found the same thing with "Fall, or Dodge in Hell" - the first part was great, the second awful. I'm wondering if Stephenson just can't handle multi-act stories.
I agree and even though I usually have a lot of complaints about Stephenson's later books, I just keep reading them for some reason. There are real high and low points. He's the only author who I've read completely and I love to complain about him.
Stephenson is just very inconsistent. Some of his work is real treasure, some just meh. He's famous for building fascinating worlds, getting some action going, but then not being able to deliver a satisfying ending (e.g. Snow Crash, Diamond Age).
Anathem is for me his only well-rounded book where he delivers on all fronts.