Speculation on What the FBI Was Doing

I approach the Michael Kelly case with some preconceptions:

1. the FBI has never been particularly fond of liberals.  The head of the agency has never been an agency.  For a long time it was headed by J.Edgar Hoover, a great bureaucrat and no friend to liberals.  It was a struggle to get some diversity into the agency, both minorities and women.
2. as an entrenched bureaucracy with its own esprit de corps it's liable not to follow direction from the outside.
3. Kelly I knew from his association with Gen. McChrystal and the Rolling Stone article, which got McChrystal fired.  I may have seen appraisals like that of Sarah Chayes in Business Insider, essentially a loose cannon, as I was once called, innovative but needing close management.
4. Not being a lawyer I've no good way of judging between claims that the interview with Flynn where he lied had no "predicate" (the Barr position) and therefore the case was tainted, and claims that the charges were appropriate and well-based.
5. Being a Democrat I'd enjoy any embarrassment to the Trump administration.

So, what do I make of Kelly, his indictment, and the subsequent dropping of the case by Attorney General Barr?

1. He was totally miscast as National Security Advisor, particularly for a president such as Trump. His selection, despite the warning from Obama, was an early instance of Trump's incompetence.
2. I doubt the narrative that the FBI looking at Flynn was part of an Obama administration's plot to undermine the Trump administration.  I don't believe the FBI would risk good relations with the incoming administration just because Obama or Yates told them to. That wouldn't fit my picture of the FBI as sophisticated bureaucratic players.
3. Not being a lawyer, I've not carefully followed the arguments about FBI having a predicate for its investigations, particularly because the rules seem to differ some between a criminal investigation and a national security (counter-intelligence) investigation.
4. My vague suspicion is as follows: in counter-intelligence people are paid to be suspicions, overly so.  Witness James Jesus Angleton, about whom I've written a time or two. It doesn't seem totally unreasonable to me that FBI agents would look at Flynn, fired by Obama from his DIA job, and say to themselves: if I were a Russian agent I might try to exploit his hard feelings, at least feel him out.  Certainly the KGB would see that as a potential gold mine and certain to reap big bureaucratic rewards.  
5. If I'm an FBI bureaucrat, I think I'd believe that the Russian/Flynn investigation could offer big rewards--it'd be good for my reputation and promotion prospects.  (I'm assuming that the FBI culture is rather insular, and  agents would believe that their director still, as J. Edgar was, could insulate them from flak from DOJ and the presidency.  )
6. I like a summary of the Mueller report from Dana Milbank: the Trump campaign wanted to collude with the Russians but was too incompetent to.  The whole episode is murky, and I don't believe it could have been much clearer to FBI agents.
7. One known unknown: we don't know what covert sources of information were and are available to the administration.   Presumably there are some, the existence of which has been hidden from the public record.

So my bottom line is disbelief in any sinister plot against Trump and his people. I think a combination of bureaucratic motives, culture, and incompetence came together with Trump incompetence to produce one good result: Flynn's resignation as national security adviser and likely a bad precedent for the way the FBI should operate in the future.