The part about the customer dress code was declared to be unevenly enforced between the Panera Cares store and the normal Panera bread store, so that seems like another issue of policy.
The Yelp comment that mentioned smell is a tough one. I was thinking about not having any place to sit period to avoid that, but then one could make the argument that isn't the Panera Bread experiment.
I applaud Ron Shaich for at least trying. I personally would not have gone towards opening four stores without proving out and refining the first experience of the first one. By just having this one store, it could have stayed open longer before closing, and the employees working at that store could have been given better job security e.g. if this store doesn't work out, then I'll guarantee you a position of employment at your nearest Panera Bread.