There are exceptions (like Bob Gates staying on at Defense), but presidents work hard to fill as many positions as the law allows with folks beholden, loyal and like-minded. After all, elections matter and these political appointees reflect that constitutional process.
There are limits, of course, some in law because of 19th-century civil service reforms and others out of practical considerations. In early 2009 President Obama changed out Mike McConnell as director of national intelligence and me as CIA director, but he personally intervened to keep Steve Kappes on as deputy CIA director at Langley. And, as per tradition, he made no other changes in the intelligence community.
Both permanent and transient elements contribute to the policy process. The permanent government brings with it fact-based expertise and experience, both of which are virtues unless they become so dominant as to foster stagnation. The transient folks bring a political legitimacy along with a vision and energy for change that stimulates progress unless they become so obsessive that it fosters recklessness.
There is a clear tension, but the tension can be creative. With ambiguous information and split counsel, presidents can be bold without being reckless, informed without being captured by expertise, as happened in both 2011's Abbottabad raid and 2007’s Iraq surge.
Now in its seventh year, it might be good to take a look at some key decisions of the Obama administration through the lens of this distinction. It could be especially illuminating since this president is known to keep his own counsel and his administration has earned a reputation as being insular and controlling at the expense of Cabinet officials (who more tend to represent the views of the permanent government).
Out of the gate, two days after the inauguration, the president promised to empty Guantanamo within a year. I was still in government at the time and we all supported the concept of reducing the prisoner population. We already had released hundreds. But IF WE HAD BEEN ASKED, we would have pushed back on the 12-month timeline as creating pressure to make bad decisions on releases -- which the permanent government was duty-bound to oppose, as it has and as it continues to try to do.
There may have been some of that same dynamic at work five years later with the Bergdahl swap for five Taliban leaders from Guantanamo. The political imperatives to clean up the Afghan battlefield (no man left behind) before the administration's self-imposed clock ran out and to reduce the population at Guantanamo led to an incredibly awkward Rose Garden ceremony with the Bergdahl family, administration characterizations that a deserter had served with "honor and distinction," and a new precedent of negotiating with terrorists that the permanent government would have to live with.
The administration routinely has shown itself to be fond of timelines, the better (I suppose) to enforce and police the implementation of decisions. Hence, withdrawals from Iraq and Afghanistan were on the clock rather than being conditions-based, the approach that would have been supported by the permanent government. Playing to the shot clock led to near disaster in Iraq (and a return of U.S. forces) and threatened to do the same in Afghanistan until withdrawals of troops were pushed to the right.
In Libya the president decided to go to war (although he later overruled DOD and directed it not be called a war to avoid triggering the War Powers Act) to overthrow Moammar Gadhafi, a decision opposed by some National Security Council members. It took seven months, but Gadhafi was killed, his government destroyed, local tribes empowered and Libya descended into chaos.