In the near/mid-term it would probably be a good course of action to have entirely automated airplanes, and "pilots" (or technicians or whatever you would call them) specialized in handling automation failures. That way, there would be no question about what their role is in the plane.
Pilots are all about handling failures - that is pretty much what their whole career is focused on. The normal operation of a modern aircraft is pretty boring - what makes a pilot worth his salary is all the continuous training and drilling that embedded emergency procedures into his mind at the reflex level... It is a lifelong process, regularly updated through new hardware and modified methods in response to incidents.
