It really depends on people, there are some decent chain stores. I have one Petco here, it's tanks are spotless, they have several full time employees that are very knowledgeable. I've overhead them asking questions about the customers tank, like how long it was set up, what was currently in the tank, before they scooped out the fish, then went on to tell them why they shouldn't buy the fish they were looking at. I have bought otos from them, they are still alive. It's the only store in my County I will buy any fish from.
I have a small LFS mom/pop store 2 mins from my house, I have never, will never buy anything from them, it's beyond gross. The other Petco and 3 Petsmarts in this County have clean tanks, but their employees are worthless.
If I want a decent LFS, I have to drive 35 mins. His tanks are clean, his livestock healthy. But know what you are buying, he'll sell you anything.