Actually, I'd say the central area of Chicago (the Loop and Near North Side) and central Boston also outrank Center City Philly, which is part of why those areas also have Apple Stores and Center City doesn't.

It's not just the fact that those areas have more affluent residents than Center City but it's also the fact that those areas attract more people from the surroudning suburbs than Center City does. Manhattan, Downtown SF, Central Boston, and Central Chicago are major shopping hubs with not just the unqiue boutiques but also major department stores. As a result, they effectively are the dominant one-stop shopping locations for their respective metro areas. Center City Philly has yet to live up to its full potential in that regard. While there are plenty of boutiques, there's only one department store (Macy's) and it's a half-one at that. Meanwhile, the other cities mentioned above have plenty of department stores. To use Boston as an example since Boston's probably the most comparable to Philly, Central Boston has Macy's, Lord & Taylor, Neiman Marcus, Barney's New York, and Saks Fifth Avenue plus innumerable smaller stores. With that high concentration of stores, it's no wonder that Apple went to Boston to open it's latest flagship store rather than Center City Philly.