Presidential automony

Insofar as Obama has a coherent foreign policy, it's been largely derided (/praised) as a continuation of Bush's policies. Drones strikes, increased footprint in Afghanistan (notwithstanding the purported disagreements Woodward cites), and drawdowns in Iraq are all continuation policies. This recent FP article about Obama's GA speech notes that:

"As powerful as the presidency is, it is still in the service of events. George W. Bush did not set out to be a wartime president until September 11th; Harry Truman did not assume office intending to be America's first Cold War president. The challenge a president faces is to read events and respond by seizing the initiative, to steer history's tides rather than merely be swept along."

The President of the United States is accorded respect as the leader of the most powerful nation of the world, yet they are subject to the whims of the Liliputians, trapped in the legacies of their predecessors and the sheer inertia of the world's largest bureaucracies. All of which makes me wonder: how free are Presidents to create, genuinely create, substantive change?

They polish policies developed by deputies. They provide guidance and direction, yet ultimately, those policies are created by others, credited to them as both a courtesy and acknowledgment that sufficient granularity is impossible. We say that Obama sets the time table for withdraw from Iraq or Afghanistan, yet those timetables are guided by objective constrains. The number of flights available, the personnel that need evacuation, the tonnage of equipment requiring transport. We say Obama delivered on his campaign promise of leaving Iraq, yet 50,000 troops remain, and enormous quantities of equipment remain in Iraq, relics of a by-gone era.

So my question is: absent an event like 9/11, absent a paradigm shift comparable to the initiation of the Cold War, how free are Presidents to shape the destinies of this country?