So the primary challenges with automation as we currently do it, assuming it works as designed (more on problems with that assumption below) is that situation awareness often when things go wrong, and that recovery is harder when things do go wrong.
In just about every simulator initial training I have seen where the pilot has never flown a jet or large turbo-prop transport aircraft before, the immediate accent is on use of all the automatic features from the word go. Follow the flight director is the universal cry by the simulator instructor. The old saying of "I can't fly but I can type at 80 wpm" applies to a great number of pilots who have been totally brain-washed into automatics.
While there has been knee-jerk advice (usually following the latest accident) to add more manual flying during recurrent simulator sessions, the whole point is being missed and that is a frightening number of airline captains and first officers simply cannot fly, or have forgotten how to fly. By "fly" I mean basic instrument flying skills in IMC without the aids of a flight director and automatic throttle. Those of fortunate enough to have flown the Boeing 737-200 series or the 727 where manual flying on line was considered SOP, usually had no trouble, if flying the glass cockpit Boeings, with disengaging the automatics and seamlessly taking control manually.
This opinion, like most Pprune contributions, is personal opinion but based on one's own flying experience over many years. I would have thought the natural progression of a training syllabus for a type rating would start with the first few sessions of getting to know the flying characteristics of the aircraft. That is vital in order to gain confidence. In essence it will include raw data non-automatics features. Once a pilot can fly accurate visual circuits without the FMC and other goodies to help him find his way in the circuit, plus be consistently able to handle max crosswind landings, is competent at high and low altitude stall recoveries in IMC and knows how to recover from serious unusual attitudes in the simulator, then the time has come to learn the next steps and that is auto flight.
If the candidate is unable to demonstrate he can fly the aircraft without blind reliance on the automatics, then someone has to make a decision regarding his future with that company.
Forget the cries of extra costs of simulator time. Operators cannot have it both ways. If they want competent pilots able to safely handle the aircraft manually as well be entirely familiar with using the automatics, then the extra costs involved must be accepted.
It reminds me of another old saying that flying aeroplanes means hours and hours of boredom punctuated by occasional moments of intense fear. From what I see, the occasional intense fear is when the incompetent pilot loses the automatics and is forced to fly manually raw data...