Engines, an excellent post as ever. Might I though take gentle issue when you say:-
Haddon-Cave identified the symptoms, but got the root causes wrong because he was fed a series of lies, including about when the cuts happened.
He was given evidence that identified exactly when the cuts happened and how they were implemented, which included the issuing of illegal orders to subvert the regs and the threat to sack those who would not comply (as mentioned by tuc above). No doubt he received a different version of events from the ever helpful ministry special advisors, but it was his duty to sort the wheat from the chaff. Instead he decided to print the Establishment lies about a "Golden Period", and so the Report became part of the cover-up instead of exposing it.
That is the bitter truth about this scandal; the Establishment in the form of Coroners, VSOs, Ministers, MPs, HoC and HoL committees, the RAF Provost Marshal, the Deputy Chief Constable of Thames Valley Police, to mention just a few, just didn't want to go there, though with some honourable exceptions. This is a scandal greater than the Dreyfus Affair in my view. Not only has it persecuted the innocent while protecting the guilty, but it has led to loss of life and wasted resources. Most damningly of all, it has seriously compromised our nation's Air Power. That is why I say the thoughtful measures that you propose must be under the auspices of an independent Regulator, ie independent of the MOD. Likewise with the Investigator, which must be independent of both, so that neither can be compromised by those who would again wish to do so.