I believe it depends on the manager/caretaker.
There is a big difference in our 3 not-so-local pet stores (I live in a small small town away from any cities)
The PetCo doesn't have any SW, but the FW is pretty well kept. They could change a few things, like not keep so many Oscars in one tank, but they do a decent job.
One of the others called Jacks is horrible. They have a large FW section and a decent SW, but the fish are always sick and there's always dead ones. Alot of the SW fish arn't very healthy, and they put species together that they shouldn't (i.e. lionfish w/ clowns or gobies). Also, the employees don't know squat, I won't go into the long story I have about that.
The other is called World Of Pets, and it's wonderful. They have a tremendous FW section, and a very large SW section. Their fish are always healthy and well kept, and they never mix species that they shouldn't (i.e. keeping a small Niger Trigger by itself because it will kill the other fish instead of cramming as much as they can in the tanks). The employees are also very nice and helpful. The manager cares about the health and wellbeing of the fish and pets at his store, and he's careful to hire employees who care and know too.
I believe it all depends on who's in charge. I've talked to the SW manager at Jacks, and she didn't know squat. The one thing I bought there was my Royal Gramma (I was looking for one, and this poor fella had just arrived and was all ready being picked on so I had to save him), and she tried to give me a Blackcap Basslet instead! The manager at World Of Pets cares though, and it definatly shows in the quality of their fish. The health and wellbeing of a fish depends on if the manager cares about quantity rather than quality, IMHO.