You're right. A handful of Captains and Majors call the shots with the ROE and the UCMJ, and the CINC is powerless to stop it.
Your lack of knowledge on this subject is evident - Understand it is not our ROEs that are the problem (per say). But interpretation conflicts that arise by the bureaucracy within the military itself.
Those interpretation conflicts coming from all different levels, be it by different commands, particular Cpt's, or as is typically the case JAGs involved with AARs.
Do you know anything about EOFs? Or AARs? - These two areas are the biggest reasons why disputes ever come about regarding the use of force. And the President can do little about each of these processes. That is the reality bud.