The President can nominate candidates for various positions, but these positions must be approved by Congress.President Obama was inaugurated January 20, 2009. At that time, his Democratic party controlled both houses of Congress decisively[1]. It was not until 2011 that his party lost the house. And in fact, his party still retains the Senate but will lose it in January 2015. But it is only the Senate that approves appointments and his party has controlled it the entire time he has been President. And if you look at the make up of his cabinet, you will see that he has been able to fill it with people that are reviled by the opposing party [2]. To say that he hasn't gotten his way on the vast majority of cabinet appointments just isn't true.
Second, the government itself is made up largely of agencies which are outside of the ability of the democracy to affect. This includes the military
The President is the Commander in Chief of the military. He exercises complete authority over them. [3] All the heads of the other agencies you listed are appointed by the President including the Federal Reserve.
Your comment is typical of the current rhetoric surrounding attempting to "debunk" the thought that the President has substantial power. The fact is the President does have substantial power and saying otherwise is merely attempting to excuse the performance of Obama that so many people are disappointed with.
[1] http://en.wikipedia.org/wiki/Party_divisions_of_United_State...
[2] http://en.wikipedia.org/wiki/Cabinet_of_the_United_States
[3] http://en.wikipedia.org/wiki/Commander-in-chief#United_State...