LJ, I see it much the same way as yourself. Where I do tip my hat to Tuc & Chug is that the MAA and MilAAIB draw all of their uniformed staff from the area under investigation and then return said staff to the area of investigation either at tourex or end of temporary detachment. In this regard the MoD aviation safety organisation is unique and it probably has a deleterious effect.
Could it be better - I believe so and have raised this point with 2 different MAA heads. The alternative structure I offered is to more closely mirror the AAIB who draw permanent staff from civil aviation. The MilAAIB should similarly draw permanent staff from military aviation (ideally FTRS) and (given the airspace is inherently a civilian/military mix) should report jointly to both Secretaries of State.
Unfortunately nobody made me Emperor so the status quo remains.