Whole Foods produce has been dreadful for years. As I understand it, that's the result of a deliberate shift from groceries to prepared foods ("stop in and pick up dinner for the night"). Amazon definitely didn't break Whole Foods produce.

Whole Foods in Chicago does a good job with meat, dairy, and beer. We more or less treat it as a specialty store for those three categories, and buy everything else from local stores. Produce, in particular, is always better at Mexican grocery stores.