There is a simple and effective solution to all this. The cyclic, recurrent and type rating simulator sessions should include a significant proportion of hand flying without the aid of automatics and that includes the flight director. Touch and go circuits and landings are very good for sharpening instrument scan on basics. Of course there are very obvious limitations to "practicing" on revenue flights, and commonsense should prevail. Switching off a flight director in flight is not exactly dare-devil stuff - although there are many who shudder at the thought.
The majority of simulator practice is on automatics when already 95 percent of actual flight is also on automatics. If the ideal is to be one hundred percent competent at both skills (automatic monitoring or basic handling), then equal time must be allotted in the simulator. Inordinate time spent taxiing a simulator to a holding point a mile away is time wasting. A landing configuration stall at 500 feet on final is not a time waster - nor is a stall recovery at 37,000 ft. These have happened yet the only time stall recovery is practiced is in initial type ratings. Even then the landing configuration stall is usually limited to 5000 ft agl for goodness sake.
Some regulatory authorities permit unrestricted use of automatics for an instrument rating test. A hand flown steep turn is about the only "test" of manipulative skills. Yet the tolerances allowed in the instrument rating test remains whether the automatic pilot can fly "within tolerances" or the pilot.
Simulators are invaluable devices for training pilots to fly aeroplanes. But if it is agreed that a high level of competency is required of flight crews both in automatics and basic manipulative skills, then operators need to stop just paying lip service to the need for basic flying skills and schedule adequate simulator time to cater for this.