One of the problems we have is structural. The constitution leaves us with a lame duck period of 2 1/2 months. One of the reasons for such a long period is the president is responsible for filling so many executive branch positions. It's not just the cabinet and white house staff that Obama must nominate but the president is ultimately responsible for filling about 7,000 positions.
My suggestion would to be to increase the civil service so that the president is responsible for appointing only the top officials in each department. My idea is very much like the British model in which the prime minister appoints only a handful of government ministers, and top civil servants compose the rest of the top levels of a UK government ministry. For example, in the UK Foreign Office there are 6 ministers while the rest of the FO is composed of civil service career diplomats. I think the US system would do well to copy this model. It would make a lot more positions free of political considerations while ensuring that the top levels of out government are staffed by career professionals and not political appointees of varied quality.
I realize that there is danger of putting too much power in the hands of unelected civil servants are who not directly accountable to the electorate. However, the benefits are many and they include a US version of the BBC satire Yes, Minister. We could call our version Yes, Secretary.