Young Paul,
If I understand you correctly, you are saying that training should be targeted at the areas of most risk to address that risk? You cite loss of thrust from both engines as an example.
I disagree to the extent that I believe that flying is a 360deg problem requiring 360deg solution. What I mean by that is that a pilot does not develop superior skills and awareness by tackling single issues. Sure, one would be more proficient dealing with total loss of trust by practicing it. But also one would be more proficient by developing a superior sense of situational awareness and general competence.
The issues of computers in the cockpit is not simply an issue of hand flying, but an overall issue of maintaining the required skills to be sufficiently aware and knowledgeable. Hand flying specifically, doesn't just improve one area of one's ability, it attunes the pilot to the nature of the environment he is operating in.
You also cite CRM as a problem. CRM is generally a problem when the F/O lets his responsibility to ensure a safe flight slide. I believe a major reason for this is lack of confidence which generates a lack of willingness to tackle unsafe practices by Captains. I am sure that an F/O who is competent in all aspects of flying and thus confident in his knowledge and ability to handle the aircraft in any recoverable situation, is not the kind of F/O who would let a Captain continue with an approach to Mangalore such that it entire approach is high and a touchdown so far down the runway that it must have been obvious the aircraft was is great danger. That is an extreme example, but even in my airline F/Os who have no fear of disciplinary action (quite the opposite) often fail to challenge Captains when it is their job to do so.
Specifically targeting high risk failures is not going to help anyone in the long run. Specifically encouraging crew to develop as complete, confident and thus thoroughly able and flexible pilots is critical. Being able to confidently take over from the automation at any point in a normal or abnormal flight is, I believe, absolutely critical to that development.