'trim it out'. I'd suggest your last point is very relevant. A two year duty cycle is far too short in the modern world and needs addressing., especially at these senior levels. Actually, given the small size and structure of the RAF today, I suspect the two year tour idea should be altered in favour of a significantly longer cycle.
I suspect that your first point is also relevant' are VSOs given enough training in project management? Really, this is where the senior engineers should be. Just because someone was good at flying and leading a unit, he/she will not necessarily have developed the skills or interests to direct an expensive long term project well. Not without lots of extra training & experience. The senior operational folk can proved worthwhile advice from their backgrounds.
Unfortunately the Civil Service has a poor record in project management too; they really don't understand money or scope definition and contract specification well. .