MMM- I have to take exception to this, at least to some degree. They would not be in business at all were the corporate mindset as you describe, though I am sure that attitude runs though the low level day to day people.
(1) Petco (and PetSmart, and WalMart) remain in business by doing something right. We may all rather reflexively prefer the "little guy" or the "Mom and Pop" shop, but invariably -
things cost more at those places.
(2) Further, you are much less likely to find current gear and equipment at the small or independent shops. And if you are not careful, you wind up paying more, sometimes a LOT more, for stuff.
(3) In terms of fish, some LFS are definitely superior to others. Most of them are superior to places like Petco, but then - not always. This is far more true with Ocean critters than with Freshwater critters. Petsmart for example, takes really good care of their freshwater fish in the stores I have seen. WalMart, at least in this area, does too.
You have to consider this, and also consider how you want to use your money. My money, at least, is a limited resource I want to make stretch as far as possible.
Personally, I don't usually buy livestock from our local PetCo, but I will buy drygoods from them. I tend to negotiate with the LFS folks for large purchases, but even then, about 50% of the time I will buy off the internet, purely because of price. DrsFosterAndSmith, Marine Depot, ThatFishPlace, and a couple others have good prices and good reputations.
I like LiveAquaria and ThatFishPlace for buying livestock off the net. I *know* what ThatFishPlace is like in terms of livestock, since I had the wonderful opportunity of living within driving distance of the store for a couple decades. They are not the least expensive, but they both take good care of their critters.
But if I saw a fish I wanted in Petco, the price was right, it looked like the tank was well maintained, and the critter looked healthy - I would certainly not hesitate to buy it.
And the best place to get fish, frags, and other goodies? Your local reef club or aquarium society. People trade good stuff around all the time. Be careful of used hardware though, people usually think it is worth a lot more than it is really worth when they are on the selling side of things.
-Paul