Training in the SIM must have direct cross-over to line flying. If it doesn't, then we might as well use cardboard cockpits to just read checklists and go through the motions.
Many people state that they will use the automatics in the real world whenever they suffer some sort of engine failure, but in my current airline they always hand-fly that procedure, and are never allowed to practice with the a/p doing the work.
Genuine 'no-fault' training will go a long way to give crews the confidence and flexibility of approach that will allow them to choose between automatics or manual flying.
Too much in the SIM is done by rote, and too many view their time in it as a stressful hurdle, sadly not the marvelous training tool it really is.