A and C:-
From the technical standpoint the RAF is cleaning the house
It rather depends which house you are referring to. I think that clunkdriver was referring to the RAF's own house (and that of the MOD), and that is certainly what I meant by it. It is all very well removing the mote from others' eyes, but first some casting out of beams of one's own is required, as once famously called for.
If those subject to regulatory authority have, unchecked, not kept to the regulations then that is a condemnation of that regulatory authority. The words breweries and piss-ups come to mind...
As POBJOY has said, there is a total dearth of trained experienced military engineers who are knowledgeable of the regulations, let alone having the ability and willingness to enforce them. Without them the process you describe is simply rearranging the deck-chairs.
It is the MAA that is the real problem. It can't do its job because it doesn't know how to. In order to avoid further suborning of the regulations, as described by tucumseh, it has to be removed from the control of the MOD. At least for starters I feel that it should then be sistered to the CAA, so that some professional expertise can be called upon in order to reform and rebuild it. Ditto with the MilAAIB and the AAIB. Then, and only then, might we hope for some authority from the authority, and some objective investigation from the investigator. It is a 1000 mile march, so best we get started soonest!