Downtown Chicago? Not really. Eataly and L'Appetito are the only two I can think of. Presumably you're familiar with Eataly. L'Appetito is a small grocery store/bakery/prepared food spot that's much smaller but has similar features to Eataly (and also an Italian focus). Other than that you're probably looking at Whole Foods. Not sure if there's a Mariano's downtown (there's one in the South Loop), but it's more akin to Wegman's. You might find online references to Fox & Obel, but it's closed.

I can't recommend Treasure Island. I've lived about two blocks away from the Lakeview one for 20+ years and I'm mystified as to how it stays in business. It's fine for staples, but I wouldn't recommend it for fresh/prepared items because at least the one near me doesn't have the food traffic to turn it over often enough.

Check out the list of Great Neighborhood Restaurants & Resources on LTHForum.