I'd like to think the sky will always be filled with big airliners complete with two pilots at the helm, but I believe the air taxi scheme will increase in market share as time goes on. The new, smaller jets are being designed to do precisely that - the Eclipse is said to have a seat cost close to a full fare airline ticket. There are still some problems with this since no one wants to pay full fare, and I doubt the seating on the Eclipse is that spacious. A realistic approach for the next 20 years, as air travel expands, (which is supposed to, they say) is a hybrid system that utilizes the infrastructure already in place. Airliners will continue to operate out of their huge DFW's and ATL's, etc. while air taxis emerge and utilize satellite airports that are currently operating well below capacity. DFW may be heavily congested, but if I live in a suburb of Dallas, why don't I just use an air taxi service at a more convenient airport such as McKinney? Advances in a vionics, automation, and datalink type systems will help facilitate the increased traffic safely. Replace is a strong word at this point, but there's a whole lot of potential here.
Another thing I often find myself pondering is the switch to the one pilot airliner. We've gone from 4 to 3 to 2...how low will we go? One of NASA's projects for the next century of flight is to provide a ground override mechanism to prevent disasters such as 9/11. I suspect the next shift in cockpit crew will be to a single pilot on board the aircraft with another pilot on the ground monitoring a group of flights. The economic advantage (assuming the capital is cheap enough)here, of course, is that labor costs are reduced. Flying of the future is less stick and more tech.
My biggest concern with the "ground control system" is that it seems to provide just another access point for malicious users to manipulate the aircraft's controls. Furthermore, reduction from 2 pilots to 1 in the cockpit disrupts the important training aspects involved of master and apprentice. Well, enough of my musings. I'm a 50 hour ppl, what do I know?