1. No selling of dyed or painted fish. There's a great store in Phoenix called the Ocean Floor, a bit pricey, but they sell dyed fish without any warnings about how this is done. Hence I do not shop there at all, which is a pity, since they could make a mint off whatever fish the zoo might want!
2. No hybrids for sale without being labelled as such. Flowerhorns, etc.
3. Clean tanks, and tanks that have fish in them marked Not For Sale when the fish are ill.
4. Knowledgable staff.
5. Scientific names along with common names on the tanks.
6. Not just the bread and butter: give me some brackish fish, some wild caught angels, baby whales, elephantnoses the size of most adult oscars. Give me a reason to buy another tank!
And while not a key to making a great store, the most fave lfs of mine has a row of tanks with fish people drop off/donate/get store credit for. The tanks are labelled as such, and the prices lower than store stock, usually. It's great to find the oddball cory or tetra in there that I've never seen before!