The first automated aircraft would probably be data-linked to the ground with "pilots" monitoring several at once, able to step in and assume remote control if necessary.
The way I envision it, the first fully automated aircraft will still have a "pilot" onboard --
but the pilot will no longer the fly the airplane --
not even via autopilot.
The pilot's job will transition to a pure supervisory & flight management role.
The entire flight will be completely automated from gate to gate. Compliance with ATC instructions and traffic / flow management will also be completely automated.
The "cockpit" will be redesigned -- supervisory controls will replace flight controls. Here I'm envisioning supervisory controls as higher-order controls for more suited for decision making rather than for piloting. More touchscreens, less joysticks.
In an in-flight emergency, the pilot will be entrusted to make safety-of-flight decisions, via the supervisory controls.