No Action

Constraints on the presidency are not limited to Congressional action (or inaction). Here's Matt Yglesias:

What I heard back was that Fannie & Freddie are overseen by an independent regulator, the FHFA, and the White House can’t just order Acting Director Edward DeMarco. When I shopped that account back proponents of mass refinancing they were a bit incredulous. Is the president really incapable of persuading FHFA Acting Director Edward DeMarco to take action that he and his advisers believe is in the public interest? Really? I’m not a huge believer in the “bully pulpit,” but it hardly seems obvious that FHFA Acting Director Edward DeMarco is some kind of immovable object of political obstruction.

See, this is the thing -- presidents really can't just order people in the executive branch to do things. I don't know about this particular case, and obviously Fannie and Freddie are rather non-standard examples, but basically that's the structure of the government. That's separated institutions sharing powers, in Neustadt's phrase. Even when it comes to the military, where the president has unusual Constitutional advantages as commander-in-chief, there are lots and lots of examples of successful resistance to presidential preferences (think Clinton and the ban on gays and lesbians, for one).

That doesn't mean that presidents can't get their way!  It means, however, that they usually can't get their way just by giving orders. The must "persuade" in Neustadt's vocabulary -- which might mean bargaining, or maneuvering, or even bullying, but it usually takes the use of presidential resources such as time, energy, and bargaining chips.

This is, of course, one of the reasons that presidents should aggressively and rapidly attempt to fill all executive branch vacancies. Having political appointees in place doesn't guarantee loyalty to the president's agenda, but it usually helps.