GREAT explanation of the heart of the issue:

Popular discontent with the drone program has built slowly as drone missions grew from 50 strikes under President George W. Bush to more than 400 under President Obama, and it dawned on Americans that remote-controlled killing had become a permanent fixture of national policy. The issue came to a head when Mr. Obama named John Brennan, who created his drone policy as chief counterterrorism adviser, to be C.I.A. director and critics raised legal, moral and practical objections. Among the complaints: an American citizen, Anwar al-Awlaki, was killed in Yemen in 2011 without due process; too many civilians have become collateral damage; and drone strikes are increasingly projecting a harmful, violent image of American foreign policy.

Right now, the Pentagon handles drones in Afghanistan, Somalia and Yemen, where the C.I.A. runs a separate program. In theory, the public might know more about the drone program if it was shifted more to the Pentagon, which, operating under different laws, has more flexibility to be transparent than the C.I.A. and is more circumscribed by international law.

But most drone strikes have been carried out by the C.I.A. in Pakistan — 365 versus 45 in Yemen and a handful in Somalia — and officials say those will continue. Hence, the proposed change would mean scant improvement in the rules that govern drone strikes.