This is a very hot topic in the civilian world at the moment. It's being driven by several very serious accidents and the FAA and CAA are on the case. A good thread discussing it can be found here. The general drift (but I guess not the whole solution) is that Upset Recovery Skills should be introduced/reinforced at all levels of training.
Article about lack of hand flying skills - FAA concerned
You should find plenty of evidence there, but try this for a start.
AP IMPACT: Automation in the air dulls pilot skill
But it is the less experienced first officers starting out at smaller carriers who most need manual flying experience. And, airline training programs are focused on training pilots to fly with the automation, rather than without it. Senior pilots, even if their manual flying skills are rusty, can at least draw on experience flying older generations of less automated planes.
Adding to concerns about an overreliance on automation is an expected pilot shortage in the U.S. and many other countries. U.S. airlines used to be able to draw on a pool of former military pilots with extensive manual flying experience. But more pilots now choose to stay in the armed forces, and corporate aviation competes for pilots with airlines, where salaries have dropped.
Changing training programs to include more manual flying won't be enough because pilots spend only a few days a year in training, Voss said. Airlines will have to rethink their operations fundamentally if they're going to give pilots realistic opportunities to keep their flying skills honed, he said.
Hope that helps.