In the case of AF447 the Commander was not on the flight deck and/or at the controls when the event started to materialise.
I take your point about the lack of recent manual flying. This over automation issue has more to it as it affects pilots across a wide range of experience. That said the Captain is the highest authority on the a/c and some say his decision of going on rest and putting control in the hands of least experienced during penetration of CB was a factor. When he returned why did he not take control and instead opted to make a few comments on the warnings? Pitch and power eluded them all for 4 minutes, yet all of them knew how to fly. Notably it was the glider man who was the one pulling back the whole time.