It varies drastically and it all depends on who maintains the aquatics department.
For instance, I am an aquatic specialist for PetCo. People think the majority of use are relatively ignorant and generally have no place in the aquarium trade. Unfortunately, this tends to be true in some cases, but not all.
First off, our systems are very limited in what they can do, so before you blame the employee, consider this first. We run very low gallon sumps with a less than desirable turn-over rate. Couple this with plumbing hooked into a culligan that runs carbon (and pumps out tap water) this instantly creates problems for the saltwater tanks.
Not to mention the fact that the some of live stock we get tends to come in hungry, sick, ich ridden, and even dead. We turn away packages containing over 50 percent dead fish, or fish who have visible ich. We cannot speak for our distributors, so before you go off ranting that petco fish always have ich, or always die, I'll be sure to refer you to the distributors, who essentially rear the fish for us.
Overall though, PetCo gets a really bad rap. I know some down-right idiotic employees who're "aquatic specialists" but you can't help this. At the end of the day, this is a business.
My store however, speaks for itself. My saltwater section near sparkles. I rarely EVER lose saltwater fish and if I do it was either
A) I didn't do the shipment (because it came on my day off) and somebody put two fish in with each other who were incompatible/or with aggressors
B) Usually only experience damsel deaths.
You will see no algae on my tanks, my corals are all open as can be and my fish are VERY well fed and taken care of diligently. Not a single fish has visible ich, fin rot, or anything of the sort. My rocks don't contain aiptasia, anything. I was told if I can consistently keep up my SW
sales, we will be trying out a completely new design for saltwater. It is apparently x100000 times better and healthier, and I've even talked to some very experienced reefers who were quite impressed with this new implementation.
It is however only limited to stores with amazing saltwater sales, and the others are being forced to phase out their displays.
All in all, don't give PETCO the bad wrap, give their AQUATIC SPECIALIST the bad wrap.