Doing some research for a story on presidential transitions, I came across this 2000 Washington Post story by Tom Ricks:
The basic problem in filling the top slot at the Pentagon in the new Bush administration is that the president-elect's defense policy already is fairly well determined, and so are most of the new administration's other top national security appointees, people involved in the process said.
When former senator Dan Coats (R-Ind.), considered the front-runner for the defense post, met last week with Bush and Vice President-elect Cheney, he asked Bush whether he would be subordinate in policymaking to Colin L. Powell, the former Joint Chiefs of Staff chairman who will be secretary of state, according to a source familiar with that half-hour-long discussion.
The president-elect responded that "the defense secretary would have an equal place at the table," this source said.
... So what does that leave the new defense secretary to do? At best, Bush advisers and other defense experts say, he would act as a kind of chairman of the Pentagon, the "Mr. Outside" who lobbies Congress and the public on defense issues. At worst, they add, he would become a figurehead--a concern that Coats expressed at his meeting with Bush at the Madison Hotel last week, the sources said.
Of course, what we saw in the ensuing eight years was an extremely powerful Secretary of Defense who stepped on the State Department's toes by taking major control of foreign policy initiatives and bypassed traditional intelligence community authority by expanding DoD intelligence gathering. And Powell was increasingly a lone voice of skepticism whose influence declined steadily. Just goes to show how much events can change a presidency, and how careful a president needs to be when selecting top administration officials.
-- Tim Fernholz