SGWB, I understand what you are saying for the people driving past, but when people get out of their cars, and cannot see the stores, nor their signs, the stores are indeed out of sight. When they get out of their cars at Grand Blvd Publix, they can see most of the store signs from the parking lot. For big box stores, it wouldn't likely matter much regarding the visibility, because people go to those stores for specific needs. However, for a small store/business which hopes to feed off of walk-by foot traffic, second floor doesn't sell nearly as well as ground level.
That said, I do like the idea of less impact on the property by parking underneath, and I certainly would like the shade of parking on a hot summer day. Plenty of shopping malls make that work by providing parking decks, where real estate is at a premium.
With reference to Kurt's point about parking in front, I, too, like some of the shopping design of places like Destin Commons and Pier Park, where the store fronts are facing other stores and pedestrian foot traffic, with parking on the peripheral. I think Pier Park is laid out better because it doesn't have as much road frontage, compared to Destin Commons.