In Flawed by Design my colleague Amy Zegart explains why the nominal authority of the Director of Central Intelligence over the non-CIA parts of the intelligence community and the nominal authority of the (pre-Goldwater-Nichols) Joint Chiefs over the armed services never really worked: they were designed by Congress not to work, in order to protect the interests of Congressionally favored bureaucracies. The Navy didn’t want the Joint Chiefs to be able to interfere with its affairs, and the War Department (which became the Department of Defense), along with the State Department, didn’t want the DCI to be able interfere with their own intelligence-gathering and analysis.
Given the current contortions over the intelligence reform bill, I think Amy has all the material she needs for a sequel.