[kelnos]

The Las Vegas Strip makes heavy use of pedestrian overpasses, but I don't find them to have the negatives you describe. Possibly because the area is so lit up (even at night), cars are kept deliberately very separate from from pedestrians (a lot of drunk people roaming around), and in many places the above-ground overpasses connect to the second levels of adjacent buildings, which makes them a more natural part of the cityscape.

I'm not sure that kind of design can work everywhere, but it can perhaps be an option in some places.