I have seen shops start out, simply organized and clean.....but over time (3 years and more) they have expanded from from aquaria to reptiles, mammals - birds, insects - amphibians. The more they expanded the more things went a bit off with organization and jusy basic husbandry and cleasiness. The mixture of all these animals, lack of space (due to expansion and over stocking materials and animals), poor up keep on the animals and not enforcing and getting the workers to keep the up keep on the animals. The bigger chains seem to make all this more pleasant but the prices are also something that make that happen. I prefer the smaller mom/pop shops but few can be pleasant to enter, like mentioned they just don' t make or can' t make it pleasant. The big thing is the smell, again funds - space - and over stocking makes this happen. Shops should special on more certain animals but if they did how long would they be around really. The few that go strong do so because of the clientele.
Just a few things I have seen in both mom/pop shops as well as the big chains:
Dead fish in tanks while saleperson tries to sell fish to a customer

Feces on dogs and cats that are about to be presented to a new interested customer or a bought animal already

Injured birds in same enclosure with interested new buyers wondering what happened

Over stocked tanks with a litter of snakes (in general) while a salesperson just adds more in the tank

Other lizards mixed together that should not be housed hours let alone days together
The list goes on, this plus the rarity of finding animals I enjoy makes me look but never buy anything from a pet store.
Again it not just one thing but once they expand them seem to loose control of the basics.

just my 2 cents.