If we approach the problem from a perspective of "How to make flying a viable commute option?" we can come up with atleast a few scenarios
1) Cities near water bodies like SFO, NYC, Miami or even Chicago can benefit from over water flying cars. This provides some safety while making more areas livable within a short commute to downtown.
2) Places like Mumbai, Bangalore where car ownership has outpaced the governments ability to create roads causing massive traffic jams can be served by a vertical stacking approach you mentioned and leap frog the western worlds freeway model. By creating pre-defined paths in the air and having only autonomous flying cars, the governments can save money on building roads, parking etc and also provide a level of safety against rogue drivers and airspace violation