1. Any bureaucracy gets less efficient over time. The US Army is a bureaucracy over 200 years old. From what I have seen, yes, the Army is awful in these ways, but better than almost any other on Earth.
2. Absolutely NONE of the gov't departments could manage their books the way Congress requires of business.
3. Simplification/streamlining makes graft and theft harder, so it is rarely done.
4. Black programs get their budgets stuffed into on-the-books programs, inflating their apparent cost or getting the "plug" treatment. This is really special, when an officer is talking to congress about his program, that had to increase in cost by 25% to hide Black Program, and he gets berated by a congressional stooge, who is read on to that program and knows why the costs went goofy.
5. More of same ^^^.
I don't have hte answer. Maybe forcing all gov't departments to comply with Sarbox and each Sec of Whatever and Congressional Chairman (House and Senate) being on the hook like a CEO for prison time if they get it wrong.