Obama was probably simply persuaded by the many-many human faces of the administration currently carrying out the atrocities (War on Drugs, NSA, foreign policy), and focused more on the soft-programs (stimulus, healthcare; and random acts of obama, that largely failed), plus got completely broken and stonewalled by an uncooperative House.
Yes, because the vast majority of them are simply the bureaucrats that keep things ticking over because they know how to do their jobs.
I've been in a number of situations where a 'bad' manager remained while new upper management was busy with 'an entirely new approach' and changing things left and right. In one case, I had the luck of being a good friend of someone in upper management, so I could discuss this issue. This manager indicated that he was well aware of the problem, but he explained that it simply wasn't worth the trouble to deal with this 'bad' manager right now, for pretty much the reasons I mentioned above.
Of course, 'right now' remained the argument, since there were always more important things to do. For all I know the guy's still there, or maybe even promoted.
Hell, come to think of it, it's very much like the code I work with. Significant chunks are a mess, but there never seems to be time to refactor. New features and 'big changes' always take priority, and somehow the big changes rarely impact that shitty code, so it stays. I'm not sure if that's coincidental.
tl;dr: apparently refactoring is avoided in most (bureaucratic) human endeavors.
As others have pointed out, the POTUS directly appoints many key people and therefore cannot be completely powerless to actually "change" policy (assuming there isn't a closed pool of like-minded people to choose from).
But I'd love to hear from someone who knows more about the Dutch system!
AFAIK it took until Carter to significantly revise nuclear doctrine, and even that was only because Carter got tired of being publically outfoxed by the Soviets.