There are so many important points that I will not attempt to select out just a few.
One major impression you are left with is that US government agencies--and no one else--control all the evidence in this case. The evidence has been described in different ways at different times, and by different spokespeople, who were often under cover of anonymity.
The public and media have had no direct access to the evidence: what we believe we know about this case is what has been doled out to us, little bits at a time. Much information has been withheld. Some has turned out to be disinformation: for example, the claim that the "chemical signature" of the water in which the spores were grown identified Frederick, Maryland, or the claim that the envelopes could be traced to the Frederick post office.
The evidence has been managed, such as during a meeting on the science held by FBI for science reporters in August 2008, when a person overseeing the FBI testimony (of Vashid Majidi) claimed to be a Naval employee, turned out to be on Battelle's payroll, and actually answers to God knows who.
The FBI's case is a sticky mess of facts, innuendo, and unsupported claims (some of which have faded away once their fiction was revealed, such as the "natural" occurrence of silicon within the spores). There is no solidity anywhere you press against this case.
Scott Shane has written in the NY Times that by many measures this has been the most complex and expensive case in the FBI's history. Yet the FBI's narrative plays fast and loose with the truth--in those few places the truth can be discerned. Hundreds of FBI agents are not part of a conspiracy. So what really happened to this investigation? How was it managed? Was it obstructed, how and by whom?
The taxpayers have bought a pig in a poke with this most expensive investigation, and it is time to inspect the goods.