I'm sure an automated system would do great in 95% of conditions but it's that 5% where you really, really need a human in the loop to make judgement calls that would be incredibly difficult to program.
Here's a classic example of a controller noticing a pilot is hypoxic, indirectly testing his competency and ability, and likely being careful with how he routed traffic around the unreliable pilot until he got better. This alone seems pretty hard to imagine automated with current technology without some overkill prone-to-failure solution.