It's the idea of complex administration, with guys on the ground 'Robotically' following instructions, which is wrong on so many fronts.
With respect, I disagree. The entire system has to work properly. What I talked about above is an important engineering requirement, (and should be) managed exclusively by experienced engineers who are required to have worked at (at least) 2nd or 3rd line on the range of aircraft and/or equipment they now find themselves with the airworthiness delegation for. In fact, this process is so exclusively an engineering discipline, it is the one area of MoD business where the engineer is required and permitted to negotiate and let contracts. (Although adminers, like Commercial, don't like hearing this). It is also the only time a company employee's appointment is formally controlled by MoD, and he is given financial delegation and the authority to commit MoD funding without recourse to the MoD Technical Agency - all in the interests of safety.
This process set the standards for the sharp end to comply with, and the primary output is a verifiable Safety Case, without which the aircraft cannot fly. One of the problems in this accident was a complete breakdown of this process, and it is vitally important to understand why because it is indicative of systemic failures. One of the reasons, almost certainly, is the reduction in engineering posts (something mentioned at the Inquest, and not confined to front line - in fact, front line have survived longer than most).
I think the underlying causes of this accident are going to be complete no-brainer. The real problem may be that MoD no longer have anyone junior and experienced enough to understand. They have plenty of senior staff who don't begin to understand. It certainly wasn't reported that anyone came remotely near the truth in court, but perhaps tomorrow we'll see if the SI got there.