Bruce, feel free to respond if I mischaracterize anything...
How does Smith portray the Cooper investigation? As an FBI investigation only or as a shared investigation: FBI, USAF, NWA, Boeing, etc. ? Does the book make it clear who was in charge of what, and who did what at various stages of the investigation?
Smith focuses on the FBI almost exclusively. When other agencies are mentioned, it normally has to do with speculation about why the investigation went so poorly.
The book does an excellent job of tracking who the Norjack case agent was throughout the life of the mystery, and Smith includes information from interviews with other FBI agents in the case. The level of detail was greater than that found in other books (Norjack, Skyjack, etc) but falls far short of the captious hairsplitting found in the online forums.
Who gets the lion's share of the blame for a failed investigation?
Smith doesn't necessarily blame anyone for the failure. He implies (strongly) that there was a cover up, not in the FBI, but in other government agencies. He doesn't claim this as fact, but his last chapter dealing with his remote viewing sessions seems to confirm this is what he believes. [I should note that I am highly skeptical of remote viewing and most paranormal claims, and dismiss remote viewing as a forensic tool. Thankfully, only one chapter of the book deals with remote viewing. The bulk of the book is based on Smith's journalism, and that's a good thing.
Smith documents the major missteps in the case, things that are obviously the FBI's fault.
Does Smith tell us what was done wrong, or what was done right, by who at critical points in the investigation?
Yes, more or less. Again, the level of detail found in the forums far exceeds anything you'll find in any of the books in the case. As such, forum regulars might be disappointed that Smith hasn't tackled all the esoteric points in the case.
Would you recommend Smith's book to the FBI as a training manual?
The Cooper case should represent a lesson in hubris and humility to the FBI. And I think they should be well-acquainted with that lesson.
However, I think the conspiracy element would cause the average FBI agent to ignore any lessons they'd find in the book. I've criticized Bruce enough on this point (it goes all the way back to our first interaction on this forum) so I feel discomfort touching on this any more than necessary.
I hope this response is satisfactory.