This is a very interesting topic and one worth discussion. It been my observation that we eventually get tactics correct, but dysfunctional HHQ relationships have long term negative consequences.
Rob posed the question of how the CENTCOM can best support the two subordinate warfighting commanders in Iraq and Afghanistan in accomplishing assigned policy goals. I'd turn the question around--do the two subordinates see themselves as accomplishing policy goals set by the national level and transmitted through CENTCOM? I'd submit that, in reality, each of these three commanders are fighting their own fights and consider the national level as their direct HHQ. I haven't seen CENTCOM given much latitude to provide significant direction to either of the commanders in Iraq or Afghanistan, except on the most routine of administrative and logistics issues.
This gets sticky because what's best to accomplish the immediate missions in Iraq or Aghanistan (in terms of resources or methods) may not be the best for the region. CENTCOM is the direct commander who should be managing and balancing the two fights--its not a case of micro-managing, but of make resource decsions where there may be a trade-off (BCTs in Iraq vs. BCTs in Afghanistan--also, there's only one JFACC for the theater; neither Petreaus or Neil owns any TACAIR outside of USMC MAGTF fixed wing) and providing left and right limits on issues that affect the whole region (Iran is an issue for Iraq, Afghanistan and the region as a whole).
The III MAF and MACV issue in Vietnam is an interesting historical note. While the Marines may have had it correct in their pacification approach, the reality is that they chose a strategy for their section of Vietnam that was totally out of sync with the rest of the theater, that had very different time and resource requirements--and they did this via a service chain of command that went from III MAF to FMFPAC to HQMC--with little regard for the joint commander. I'm not arguing right or wrong, but it was a heady bit of institutional insubordination.