Clearly, the FBI made many errors. That's understandable for a large, unwieldy government agency dealing with a complex and unprecedented crime.
The issue is the difference between incompetence and malicious intent. You seem to imply, if not outright declare, that the FBI intentionally obfuscated this investigation and conspired to protect the perpetrator(s). That is a bold stance that requires a much higher burden of proof than mere institutional incompetence.
I'm not intentionally implying anything, Chaucer. Rather, I am showing the mix of organizational behaviors. There was some incompetence, some bureaucratic turgidity, a noticeable lack of critical thinking, and perhaps some malfeasance.
Some issues present several of those dynamics at one gulp. Take the cigarette butts. Perhaps their loss can be attributed to the notion that the FBI Crime Lab thought there was no further use for them - I chalk that up to a lack of critical thinking on the part of the lab tech who wrote that memo suggesting the butts could be destroyed. Then the case agent Charlie Farrell deserves some blame for NOT insisting that the cigs get preserved AND delivered (finally) to Seattle instead of residing in Las Vegas. Then perhaps there is an element of cover-up since no one has gone looking for the cigs - as far as we know. That could be an intentional act to protect a suspect, or an intentional act to protect lousy cops from institutional reprimands.
Chaucer, I agree, the charge that the FBI intentionally participated in a Norjak cover-up is an extraordinary accusation and would require a very high level of proof. I am not suggesting that here. Rather, I am suggesting that it might be a partial explanation for the many inconsistencies and bad police work in the FBI's investigation.
For me, the most egregious finding is the loss of the larger shards in those Plasticine envelopes from the T-Bar recovery operation. To date, I have not heard one single plausible suggestion on how that happened. Ralph Himmelsbach refused to answer this when I asked, and sent Jerry Thomas to tell me that everything found at T-Bar was sent to Seattle. Compounding the problem, the case agent at the time, Ron Nichols, refuses to address this issue and continues to stonewall me, both at his Seattle home and down in Palm Desert. In fact, Nichols has never spoken to a single journalist, not even GG. Nichols won't even talk to Galen Cook, and he's generally beloved at the FBI.
When I drill down into the nitty-gritty of Cooper, it seems that every outstanding issue has problematic responses from the FBI. Take the flight path - no one from the Bureau talked to Cliff Ammerman. Take the ground search - did it really take two days to get a team together and enter the woods at Amboy? Take the money find at T-Bar. When I asked Dorwin if he, as the new case agent for Cooper in Portland, ever follow up and comb the riverbanks for more money or talk to fishermen and home owners on the Columbia, he said, "No."
Currently, who in the FBI has followed-up on Tom Kaye's findings over the past ten-plus years - the titanium, the rare earth minerals, and now the diatoms. Whenever I asked Ayn Dietrich-Williams - the PIO during these years - what her Cooper people were doing with Tom's contributions, I got the vaguest of "We're evaluating all the pieces of evidence that come to our attention...." And yet she was very happy to tell the world that Uncle LD was the "most promising suspect" with nothing more than a cockamamie story from an Oklahoma undercover FBI guy who couldn't even find Lynn's driver's license.
Bottom Line: How does one best characterize all of this? It's a mish-mash, I say.