Part of the FBI's problem is the extreme centralization that took place under Bush and Mueller. It was formalized as the Deep-State's political DC police force.
One simple change - Take away the FBI's guns. If it needs to take down a group of armed bad people, force them to coordinate with local police and their weapons, or the US Marshals.
You are correct in identifying much of the problem as “centralization”.
Historically, almost all cases were run by the local field office working with the local US attorney’s office and this avoided politicization as cases were more likely to reflect local values.
This began to change during the Clinton years when local offices were instructed that certain types of cases, meeting a criteria for political sensitivity, were supposed to be reported up the chain. The number of bosses and levels of bureaucracy in most federal agencies is staggering and the slightest mistake can effectively derail the climb up the ladder (same for military) so the front-line supervisor and all the middle layers of management are only too happy to kick it up the chain.
This means that outside of normal cases you end up with everything “sensitive” being run by a small group on the 7th floor of the FBI and/or the heads of departments like civil rights or public corruption at the DOJ. It makes it far easier to act in a political manner if you are steering the ship and deciding when to open and close cases.
We need to disperse the federal government to help decentralize it from the DC bubble - it won’t fix all the problems but in the current construct it seems impossible to even begin to fix it by keeping everything so centralized. Building a new gigantic HQ in the beltway is NOT the answer.