Bush was too trusting, he should have cleaned out all the rats nests at State, etc.... but when you look at history most departments in our government have been too top heavy and the little guys are afraid to put their careers in jeopardy to stand up....unless, of course, it’s a GOP administration they can damage; that makes you a hero in DC circles.
Bush couldn't have "cleaned them out" because there is a law protecting non-political appointees from being fired. That's called the Civil Service Law.
Over the years, agencies like State, DOJ, and EPA have become increasingly liberal, because conservative employees tend to migrate to the private sector, while the liberals become more entrenched and move up higher in the chain, getting more authority and influence.
It is a problem any Republican president will face, and it is one that Reagan faced as well. The only way I can see solving this is to radically reduce the size of some of the departments and/or combine them, while allowing no new hires and getting as many people to retire as possible. This, of course, would be heavily resisted by the employees union.
And even then, how many conservative scientists are you going to get in EPA? Anyone worth his salt is going to work for corporations, not the government.
Many of us have said that over and over.
The key here is to learn from our mistakes. When we get back in, time to gut every commie institution and their followers we can, and fast.