"That sounds fairly achieveable to me, so surely there must be limitations to the systems?"
Yes. For example, the aircraft arrives in the holding pattern, sets up for an approach, and the runway is blocked. How do ATC manage the stack?
Or, there is an on-board medical emergency requiring the aircraft to divert immediately, or a fire, or a disruptive passenger endangering the aircraft from within the cabin.
In cases like these, who re-programmes the aircraft? ATC? Ops? The FA? Or the senior passenger?
Airlines need a pilot to blame. In the event of an accident, a pilot who has made a mistake can be given the blame, be fired, the airline announces it in the media, gets a new pilot and carries on. If there's no pilot in the new, much publicised, all singing, all dancing "Blunderbus" and suddenly there's an accident because something went wrong with the aircraft, what does the airline do? Sell the fleet?