Sure, it's a wild-eyed, silly idea. But I'm using this space to think aloud and just found it funny that while our places of business are 3-dimensional, our access to them are only 2-dimensional. That seems somewhat short-sighted, no?
But in major cities, it's not 2-dimensional.
Badge already pointed out that there are a lot of multi-level roads in Chicago. Lower Wacker Drive, for example, acts almost as an "express" to get through the city from I-290 to Lake Shore Drive, whereas if you're on Upper Wacker you're dealing with lots of pedestrians, traffic lights, cross streets, etc.
Much of public transit in these cities in underground subways, and in some cases you can get directly into businesses without going back up to ground level.
Major cities are already 3-dimensional in ways that you're completely discounting because they don't fit your picture of what 3-dimensional means.
I'd venture to say that the failure here is one of imagination. City planners across the entire world have been trying for a hundred years to try to optimize designs in order to improve the way cities flow. The Chinese, as one example, can simply dictate how a city should be constructed and if you look at the recent and massive growth of cities like Shanghai, you know that in many of these cases they can design almost a "blank slate" and construct it without worrying about impact on legacy systems.
Yet... Nobody, across the world--being the experts in their fields with the most incentive to get it right and make their cities more functional--is implementing your idea.
I guess they're just short-sighted, unlike you...