Opinion Journal has a great article on Bush vs. the Federal Bureaucracy today. But don't let the word bureaucracy scare you off - this link gives you the big picture.
http://www.opinionjournal.com/wsj/?id=110001922
Excerpts:
The permanent bureaucracy, which Henry Kissinger once accurately described as the fourth branch of government, resists change. Harry Truman knew this well. When he turned over the presidency to former Dwight Eisenhower, he remarked that Ike, who was accustomed to having his orders obeyed, was going to get a big shock when he issued an order from the Oval Office and nothing happened....
President Bush, faced with multiple crises, is no doubt learning this sobering lesson. His Forest Service, taken over by "environmentalist" dilettantes during the Clinton years, is helpless as dead wood accumulated through years of neglect fuels fires that are destroying many thousands of acres of forests, endangering people, animals and homes. Justice Department and Federal Trade Commission lawyers, emboldened presumably by recent corporate scandals, are having atavistic spasms, hunting down companies that are either competing too little or too much....
And so it goes. Mr. Bush is somewhat in the position of trying to steer an 80,000-ton supertanker with nothing more substantial than a sailboat rudder. He is rueful about the difficulties. When the Environmental Protection Agency undercut his Kyoto policy with a report asserting that the globe is certain to be warmer than now in a hundred years, he brushed it off as yet another vaporous emanation from the EPA bureaucracy.