The issue is not so much one of basic pilot skills being substandard, more a case of economics driving aircraft to fly autonomously at the edges of the flight envelope. When the equipment fails, pilots are placed in the position of having to take over control of an aircraft at the edge of flight stability, frequently with degraded instrument indications or artificial control constraints.
I am inclined to believe that in general, pilots cope admirably with these failures in most instances and that we should be witnessing a lot more of these loss of control type incidents than has been the case to date.
That said, there is certainly no cause for complacency and pilots should be encouraged to fly manually whenever possible. Perhaps the lowering costs of fuel might allow economics to take a back seat for a while?