DoD does have large problems with procurement IMO. Parts of it are self-inflicted (e.g. by making it nearly impossible for a supplier to be "certified" you give existing suppliers the ability to extort more money from you), parts of it are inflicted by the government (e.g. various HR laws the gov't self-adopts in order to 'lead by example', requirements to buy stuff the DoD doesn't even want, etc.)
But the big rub is that it's a very hard problem to tackle. There's already tons of rules and regulations to try to prevent the issue of corruption. Adding more rules makes the 'normal path' even less efficient. Taking rules away risks lots of graft in the 'worst case path'.
And even if DoD somehow adopts a most-efficient acquisition scheme, it still has to get the prime contractors to become more efficient to actually realize savings based on this. There's only so many defense contractors to choose from for major acquisition projects, and from the DoD/nat'l defense point of view it's better to buy expensive kit than to stop buying at all for a few years into order to weed out the most sluggish contractors.