Stephensen has been stepping incrementally closer to being a literature author with each book he's written. Snow crash is fluff, Cryptonomicon is pretty deep, and the Baroque Cycle is a master work (in the original sense). Anathem is his first post master work book.
Many posters have made the claim: "It would be better if you removed X", for various values of X. What is instructive is that not everyone agrees on X. Stephensen had a lot to say in this book, on many topics.
I'll address a few things here, but this list isn't exhaustive:
* Unresolved plot elements are not bad. Only in very bad fiction does absolutely everything happen in service of the ultimate confrontation. Some things just happen, and we learn about the characters in how they deal with them.
* Characters exist for themselves, not the plot. If every character was there 'for something', this would be a (bad) video game, but it isn't, its a book.
* The ultimate conclusion of the book is that intellectuals have a duty to the world to remain engaged. The first half (roughly) of the book exists to convince you that being segregated would be lovely, while the second half drives towards the negative consequences of that approach. The character development and the plot both work to develop this theme over time.