For me, things that bug me and make me not go back to a pet store are:
(like Lins said) staff that don't know what they're talking about/pushing certain products that aren't actually what I need, too small cages for small pets who need large cages (guinea pigs, rats, etc), puppies/kittens (dumped "rescue" puppy/kittens are a little different, I'd prefer them to puppy/kitten mill animals), nasty aquarium areas, etc.
My favorite pet shop (well, it's really a "pet food boutique") sells organic/grain free food, locally made pet toys, if you ask for a certain food the owner will start stocking it for you, and the owner will order whatever you need if you ask her. Basically, I feel welcomed into her store and I enjoy it there rather than wanting to get out asap because of something - the smell, annoying workers, whatever.
She doesn't sell animals but if you ask, she'll help set you up with a local adoption agency to get you whatever pet you want. Or, for pets you only really find in pet stores, she has a list of good stores and bad stores so you know who deserves your money.
She also charges barely over the price she buys an item for, no huge mark ups like at chain stores. It's the same for stuff she orders for you, she won't charge you much more than she paid for it.
I don't go there anymore because a chain store started selling the big cans of feline "Wellness" for cheaper than she does. She also had mostly fish based wet food which my cat is super allergic to so I wasn't able to get my cat as much variety as I wanted from her. It's a bummer, I really liked her.
If a store I liked had education classes on an animal I as interested in for a reasonable price, I would definitely attend.
Alternatively, if a store had representatives from rescues come in every once in a while and do presentations on a kind of animal with adoptable animals of that kind, I would definitely go.