As Tom Ricks points out, quite compellingly, in the first chapters of his new book, The Generals, what we have witnessed since Vietnam is a slow, steady, deconstruction of accountability mechanisms for the military that reached its high point under Bush. Now one of the distinguishing features of Obama is his subtle, skillful reversal of these precedents - in a way which was at once non-confrontational and beneath the radar of political Washington. The Petraeus case is an excellent example - he was denied the post he most cherished (chair of the JCS) and instead given CIA. But he was required to set aside his uniform and give up his entourage of 50 (amazing!) who followed him in his final appointments. He was denied "special" access to the White House and the president while he ran CENTCOM and Afghanistan. He and other generals were told to treat the chain of command seriously.Much of this was possible because Obama kept Robert Gates on as Defense Secretary for the first 3 years or so of his administration. Gates was a Secretary of uncommon stature, as firm as he was intelligent and the Generals feared him. I really don't get the sense that Leon Panetta has Gates gravitas.
Obama also has become the biggest general slayer since Harry S. Truman. He fired Stanley McChrystal and now David Petraeus, the man who flogged rumors about his own suitability for high political office. I don't see anything remotely Machiavellian about this. It was all rigorously application of good governance principles and rules of command authority. But the result we are now coasting towards is an unwinding of the distortions introduced by Bush and a restoration of America's historic notions of civilian-military relations - under which the generals are to be kept firmly out of politics and clearly accountable to elected civilian authority.
Obama, by the way, doesn't get enough credit for his truly impressive leadership which always shines in moments of crises. Hurricane Sandy was just another example, and Republican Governor Chris Christie will attest.