Stephen,
You raised an important issue, but I agree with only part of your conclusion.
You are absolutely correct that FADEC presents a different paradigm to the powerplant mechanic. Today, no doubt there are many A&P's in the field who have never seen a FADEC, and would be rather lost the first time they encountered one. That'll change over time. But you are correct that it does currently present a potential obstacle for the aircraft owner/operator.
About added complexity for the A&P though, I have to disagree. It may appear complex now since it's still unfamiliar, but really FADEC makes life simpler for the A&P as well (although it may have a negative impact on the A&P's income). There's nothing to twiddle with. No set screws, no parts that wear out all the time, no fine adjustments to be made. The system is self-calibrating. Just like modern cars, gone are the days of the "tune-up". The system has a finite number of components (ECU's, sensors, injectors...) and the A&P doesn't go inside them. The A&P doesn't need to understand the internal design of an ECU. When on a rare occasion a component in the system fails, you replace it. It is generally not difficult to isolate the failed component, and in most cases the ECU will actually tell you.
So I guess I'm agreeing and disagreeing. Yes, A&P's will need to update their skills, and that will take time. There may be some hiccups along the way. But it's a step in the right direction.
P.S. Looking at your user name, I presume you use Mac OS X? To draw an analogy, imagine taking a computer technician who has worked on DOS systems for 20 years, and put him in front of a Mac OS X machine for the first time. I'm sure he'll be lost at first. But if he has the willingness to learn, he can become proficient with the new system very quickly, and will probably then recognize how it is vastly superior.