The FCC probably responds to special interest groups because people there want job security and a larger budget, and satisfying special interests will encourage those special interests to influence congress in ways that increase the FCC's budget and stability.
With some agencies (e.g. the patent office) there is also the problem of employees on a career path to work for the special interests group (e.g. get hired as a patent lawyer).
These problems can be partly solved by higher salaries and by eliminating democratic control over the agency (this has been mostly done for the Fed and for judges), although that doesn't do anything about the agency's desire to increase its power (I wouldn't expect an independent FCC to turn more of the spectrum into a commons).
A more ambitious solution is Robin Hanson's idea of Futarchy (http://hanson.gmu.edu/futarchy.pdf), where factual questions are decided by markets (e.g. will turning this part of the spectrum into a commons increase GDP or some measure of equality such as the Gini coefficient 5 years later? will invading Iraq reduce the number of deaths caused by terrorism over the next 5 years?). The role of democracy would be to figure out what measures of wellbeing should be maximized, with congress and/or agencies being instructed to follow whatever rules the markets said would maximize those measures.