The UN recently released a report recommending that American UAVs in Pakistan be under military, not CIA control. The UN believes that this would reduce civilian casualties, because U.S. UAVs controlled by the military usually have a lawyer standing by, who evaluates targets below, and vetoes the hit if it is believed it is somehow illegal (or there is too great a chance that civilians might be hurt). This is the main reason why the CIA controls the UAVs in Pakistan. With a lawyer in the loop, many HVTs (High Value Targets) get away. Not because the lawyer vetoes the strike, but because of the time it takes for the strike to be discussed, and sometimes headedly debated, delays the firing of the missile. Frequently, by the time the order to proceed is given, the target is gone.
The Pakistanis also prefer the CIA to control the UAVs, partly because this enables them to tell everyone that there are no American military forces in Pakistan. But mostly, the Pakistanis prefer to keep the American lawyers out of it, and get on with killing the terrorist leaders, and their followers, who are killing so many Pakistanis. War is hell, and bringing lawyers in is a response to political and media, not military, needs.