has anyone done the "RustyTheGeek" method (return the camera and get a new one) or approached Canon service with specific repeatable test conditions using valid comparisons with bodies such as 5D2 and 6D? the more specific you get, the more likely we are to obtain a specific statment from Canon regarding this behavior. For example, if Canon service is asked to fix the issue where "the 5D3 AF takes 2 seconds to confirm and fire the shutter while the 6D appears instantaneous under the same conditions while acheiving accurate focus", then Canon has to confim yes or no that the Camera is performing up to its specifications.
There are a number of explanations that could apply, but given that RustyTheGeek is now satisfied, having acheived AF speed improvement with a different camera, one explanation is that the issue is addressed with newer hardware and that the issue just silently goes away with newer bodies. We have no proof that this is the case, mind you, but emperically this is valid postulation. the implications could be as interesting as a manufacturing defect or parts quality problem that was addressed and Canon chose not to recall any bodies but fixes them silently as they come in for repair. It could have been a consious decision based on the cost of warranty claims. Treat this postulation as CR0, naturally