A New York Times article on recent mishaps posits that instinctive reactions to pending emergencies may actually make the problem worse.  After noting the memorable feeling of stalling an aircraft:

What is harder to remember, in the heat of the moment, is the proper way to regain control of the aircraft…

“You have to overcome what your instinct tells you to do,” said Mr. [Jean-Pierre] Otelli, whose book “Pilot Errors, Volume 5” was the first to publish the unedited transcript of the Flight 447 cockpit voice recordings.

For the hundreds of pilots he has trained to recognize and recover from an aerodynamic stall, Mr. Otelli said, “the first reaction of all of them is to pull back on the control stick” and drive the plane’s nose higher — a move that only exacerbates the problem. “It’s a reflex that’s almost uncontrollable,” he said.

The article finally notes that, despite the headline, instincts aren’t a pilot’s enemy.  The pilot’s instinct simply needs to overcome the human instinct.  Then, it isn’t hard to remember “in the heat of the moment” the proper way to fly the aircraft.  In fact, it becomes an automatic response.  Of course, such a mindset replacement requires training — something that in some cases is surprisingly lax.  The reason?  Computers do most of the flying.

Among those challenges, safety experts said, is making sure that, as pilots are trained to use these new technologies, they don’t become so reliant on them that they are unable to recall the proper manual procedures when the high-tech tools fail…

The article notes the successful landing of the US Airways jet in the Hudson River in 2009 as an example of just plain good piloting skills, which may be suffering in the age of increased automation.