Former Commerce Department Deputy Under-Secretary Derek Shearer has an interesting solution for problems (including finding a secretary) with his former department - get rid of it! The commerce department as it stands doesn't fit together well at all - there's the Patent Office, the National Institute of Standards and Technology (NIST - formerly National Bureau of Standards), the National Oceanic and Atmospheric Administration (NOAA), the Census Bureau, and more bits and pieces. A lot of science and technology, analysis, statistics, and economic policy stuff. But there is little in the way of a coherent mission for the department to put all these pieces together, and the political nature of cabinet-level departments is far from suited to the objective work that many of these components of the department do in their day-to-day operations.
Most of Shearer's recommendations make a lot of sense to me: turn NOAA and NIST into independent agencies, and move the statistics organizations (the Census and some economic analysis groups) into another independent agency, "USA Statistics". NOAA is by far the largest component of the Commerce Department now anyway, and is treated almost independently as it is (Obama proposed a NOAA head before selecting a Commerce Secretary, for instance). NIST deserves far better than it has received under DoC auspices - its Advanced Technology Program (which has morphed a few times since then, and never been properly funded) sounds like it would fit well with the Discovery Innovation Institute idea promoted by the National Academy of Engineering, and could be given much freer reign outside of a cabinet department. And keeping national statistics well away from political influence is a wonderful idea.
Shearer proposes to preserve the rest of the department in a new "Department of Industry and Trade" with a broader international focus. I'm not sure that would have a coherent focus any better than the current Commerce Department, however. In my opinion, the best approach would be complete dissolution or merger. If dissolved, the Patent Office also could be an independent agency, and other appropriate parts could go to existing departments which might have their purposes slightly expanded by the change. Candidate departments for a merger would be Labor or Agriculture, both of which are much larger than the left-over parts of Commerce would be. Commerce has long had one of the smallest budgets among the cabinet-level departments, and removing NOAA, NIST and the Census Bureau would leave it at less than $1 billion/year (aside from the PTO which is self-funding through patent and trademark fees). All else equal, a smaller cabinet would likely be more effective.
Anyway, this would require congressional action to rearrange the department, and it can't be a high priority of the administration, but Shearer's proposal definitely sounds worth pursuing once more important issues have been settled.