Indeed the Royal Naval Flight Safety Accident Investigation Centre (RNFSAIC) could perform the military role in concert with the AAIB - these professionals work closely together and are similiarly trained, so interoperability is not a problem - and they will deploy! Put them together as a joint unit, outwith the MoD's chain of command and you could have a professional accident investigation unit that LEADS the investigation from a dispassionate and objective viewpoint - rather than the purely 'technical advice' the AAIB/RNFSAIC presently provide to BsOI/SIs (whose members are untrained accident investigators). Rather sadly, this way forward was recommended by the Tench Report in 1986 (!) but it was 'buried' by the MoD for reasons unknown. Goodness knows how many lives and aircraft have been lost because of this MoD failure.
Implementation of the airworthiness regs is another subject, though closely linked. Chug is right, the MoD continue to prove that self-regulation has failed. It is now time that this function is removed from the MoD's grasp.