Part of the problem is the sheer amount of things going on. There are a variety of threats to civilization, numerous characters to follow, and it's all of a worldwide scope. Once series of chapters uses three different characters to show the bio-nano-ization of three different cities. Think of it as parallelling orchestral variations on a them. This is all really interesting, and fun to read. But it's a lot of work to keep track of everything, and it never really pays off.
The worst of it happened on page 411 of the copy I was reading. The radio-astronomer has the following quote:
"I surmise that this is a map from light-years ago -- or at least light-minutes. A great time ago. It will take me a while to figure it out."
I'm sorry... 'light-years ago"? As if light-years were a measure of time and not of distance? This is inexcusable. How does something like that make it past an editor of a sci-fi publisher? If it had happened on page 11, I would have simply decided not to read the book. I suggest that you do the same.