Daysleeper I think what the schools are turning out are capable, if inexperienced, IR rated pilots, with a minimum of hours and a new licence who are familiar with single crew Seneca/Cessna310 types of operation. The problems can start when they get their first airline job and are suddenly thrust into a multi-crew automated flight deck environment which, by design, encourages automated flying, their recently acquired skills then get rusty and the experience bank they have to fall back on is not so deep and in a totally different type of flying. Those of us who have had the benefit of twenty odd years experience of relatively unsophisticated aircraft should have no problem reverting to basics when required so an area that perhaps needs to be looked at is appropriate continuation training for new pilots coming from the flying schools and going straight to the advanced and automated flight deck?
More generally, in order that we don't find ourselves at cross purposes, I think it is important to identify just which aircraft we are talking about, as , with most modern aircraft a high degree of knowledge and expertise of the automatic systems is required if they are to be used to their full advantage. On the other side of the coin we have such aircraft as the BAC1-11 and the B737-200 where I seem to remember that all approaches were hand flown, in fact all flying below 10,000', since the automation available was very limited and amounted to Hdg Hold, Alt Hold and VS. I don't remember the VOR/LOC function ever being satisfactory!
As I mentioned above, many of the newer aircraft are automated by design, not just for normal operations but also to cope with the majority of abnormal situations too, now that there is no Flight Engineer, deliberately reducing to an absolute minimum the occasion when you might find yourself with no alternative but to hand fly. Two engines out on a four engine aircraft is one, (B747), also unscheduled stab trim input with both channels inoperative is another and the most probable, I think, might be structural damage that takes out hydraulic systems. They have all happened but can hardly be described as common occurrences and the relevant hand-flying that needs to be practised the most is with the above mentioned scenarios present.
Hand flying a serviceable aircraft is of course essential to maintain IR skills, skills that will be most in demand if things are going wrong and the auto-pilot won't work and should, in my opinion, be practised whenever it can be done without eroding any safety margins and I don't believe there can be any SOP that covers that as every flight is different. With my last employer we were told to take the autopilot at 400'agl when departing LHR but this was on very heavy B747s and designed to ensure that our tracking was sufficiently accurate to avoid ringing any bells! A trial period showed that this procedure worked the best. That was the only auto pilot SOP I have encountered, other than for CatII/III operations.