Is "Interagency" the right question?
In many ways, interagency coordination ain't bad.
The salient issue is arguably the lack of fundamental capabilities / effectiveness of individual agencies, not the coordination of the capabilities that do exist.
This is not a revolutionary observation. Many potential aspects to the "solution" from Goldwater-Nichols II to "J"PME on steroids and re-org of civil service. Many horror stories re the 90-day wonders on mega-differential pay and hunker-down-in-the-Green-Zone mentality. Some points of light from the Treasury guy with huge brass ones and the Commerce gal who could take down a bunker. But all solutions must revolve around the art of the possible and be sustainable during the intermittent periods of peace.
Rather than interagency, what do we do about the agencies?
Capabilities Not Coordination is the First Step
Though I will most certainly admit the coordination could be much improved, I believe an "interagency Goldwater-Nichols" has a chance in hell of passing in Congress. Too many rice bowels and way too many committees to get through.
Goldwater-Nichols began the process of reorganizing the Department of Defense in 1986 in an attempt to create a true Joint capability. We have made great strides but there are still issues to be resolved. That’s 19 years and we still have progress to make. We can ill-afford to wait 19 years to sort out the interagency mess.
I would suggest that we beef up the capabilities of the most critical Small Wars capable non-DoD agencies. We (the military) end up taking on all the national power functions simply because we are the only ones “in-country” with adequate command, control and communications assets; planning capabilities (to include a process), rolling stock, and security. We also bring a hefty humanitarian capability, though designed to address the medical and logistics needs of our troops.
We will always provide the security but need the others to pick up the rest. (Though OIF has provided a possible harbinger - contract security...)
There are other problems of course – some agencies will not enter a semi-permissive environment, personalities, food fights etc. - especially at the national level. These of course trickle down to the operational level and affect planning; which of course makes tactical execution difficult at best, chaotic at worst.
Food for Thought - Col. Wilkerson Speech
Audio / video of speech and Q&A: Colonel Lawrence Wilkerson on the Bush Administration’s National Security Decision Making Process. COL Wilkerson is the former Chief of Staff, State Department, 2002-2005. Text of the speech can be found here.
On edit: Here is a link to the SWJ's Interagency Operations page in the SWJ Reference Library.