I really think it comes down to how new each store is & how big the building is, as far as the number of products carried. I would say the Petco & Petsmart stores nearest me are about the same in accordance to cleanliness. The products range between the stores. Neither carry the food I feed, Innova, but a locally owned store does - all the better, but I don't buy a lot of other things at the local store because their prices are sometimes high - but they also make space for cats & dogs from the local rescue.
I think Petco started carrying some of the Cloud Star line about 6 mths ago, but I have several options for that line -- my holistic vet has carried it for several yrs, that's where I was introduced to the products, plus 2 local pet stores carry it & so Petco is usually my last choice. I'm big on supporting the small local business person
What I hate is having to hunt at more than one store for the item I most want.