I think you have a good point about the autonomy of the officers being a strength and a weakness. It is my impression that the leaders who came of age in the cold war were still geared towards fighting the Soviet Union and hoping for their war to be one of giant flanking maneuvers in large open terrain. I don't think they anticipated or were particularly interested in counterinsurgency. Unfortunately, that is exactly what they got. When you're fighting a big, evil, conventional opponent, you can get away with leadership via email, because the small unit leaders know their job. In other words, the autonomy of the subordinate officers had very few downsides. But, when you're conducting operations that your subordinate officers know little if nothing about (such as counterinsurgency) then you've got to be hands on, interacting with the civilians, observing the troops, and staying knee-deep in all operations, because the smaller unit leaders need guidance. Every company commander was pulling his hair out as he took his best guess as to how to run his sector, knowing nothing about the task that he had been given, resulting in totally different standards of behavior for the civilian populace as they traveled from neighborhood to neighborhood. Among the civilians, this caused confusion, frustration and a loss of confidence in the abilities of the coalition.
Empowering leaders is a great thing, but only if they have been properly trained. This mission, early on, was one for the Special Forces, Civil Affairs and Psyops - and there was a large number of those folks here. But, they were used almost exclusively for capturing high value targets. I think that it should have been the other way around. The SF folks know how to build a rapport with indigenous people, work with them and advise them. The regular infantry folks know how to kick a door in and grab or kill whomever is behind it. Unfortunately, our missions were flip-flopped.
But over the long haul, this can only be good. It's not the most desired form of training, but "on the job" training IS training, and people do learn from their mistakes. For ex., the Army already figured out that in the "new" volunteer Army in a war zone, everyone must be completely combat ready---there are no "specialists" who just serve meals or do communications. It already has adjusted its training regimen---whether enough or not, we'll see, but this has been the approach of the Marines for some time.
Afghan/Iraq will create a generation of unmatched military leaders---I dare say, the result will be a corps of officers that surpasses the Mexican War group of Grant/Lee/Sherman/Longstreet/Stuart etc. These men and women will be trained in counterinsurgency like nobody's business.