Long term the way we currently do air traffic control does not scale to a much higher volume of planes. The current way of doing this is super stressful for pilots and controllers and relies on decades old technology. With autonomous planes, there will be a need for managing those that doesn't rely on such technology. ATC having conversations with some AI in a plane over a radio does not make sense.

The solution here is adding more automation and moving away from the way things have been done in the past century. Ultimately, the congestion has more to do with pilot and controller situational awareness and stress levels than with the air actually being congested.

As for physical places to land, that's a much easier problem to solve. Vtols basically need a glorified parking or some kind of field. Small planes need short runways. 3000 feet would be plenty for a lot of those. Less possibly.