The thing about the national chains is that they have standardized care for the animals they keep. They have policies in place that the managers should enforce and if that happens, it shouldn't matter how brain dead their slacker employees may be, the animals should receive adequate care.
In general, from what I've seen at the Petco and PetSmart in my area, that is the case. The fish all look more or less healthy, although they'd look better in a well cared for tank at home, as opposed to the aquarium system they have at the store.
The problem comes in when inexperienced fishkeepers and low-paid, sometimes overworked wage slaves come into contact. It's not always pretty. Sometimes there are knowledgeable folks working there, but it's really a crap shoot.
Additionally, you have people who come in during the busiest time, say Saturday afternoon, and try to tell the staff what's what. When that person has absolutely no clue whatsoever. I've heard belligerent customers spouting bilge about this fish and that, and were completely off base.
So while the chains aren't perfect, they're better that some LFSs I've seen when it comes to fish health.
Wal-Mart is a whole other story though. They're atrocious unless they have someone who cares behind the counter.