I do think I disagree somewhat that this is just about money/ethics.
I never said it was as simple as money. But it definitely is about ethics. Btw, I'm using the word "ethics" in the same manner that you're using "moral", but I figure "ethics" is a less polarizing word to use

The point about caging breeding animals in puppy mills is part of breeding ethics. But the larger point I'm making is this: We have millions and millions and millions of companion quality animals being tossed around the rescue system. A large majority of those animals will never get adopted out. They will get killed. To add insult to injury, BYBs and puppy millers create puppies for the sole purpose of companionship. Thus, in today's vastly overpopulated society, one should only breed an animal to create more exemplary examples of that animal. In other words, if one were breeding a Doberman Pinscher, that Doberman Pinscher should fit the correct type, health, temperament, and possess adequate (preferably, strong) working ability. In other words, a breeder should only breed to "better" the breed. In essence, it'd be unethical to produce puppies for the sole purpose of companionship when there are millions of companion-quality puppies languishing in shelters. But BYB's and PM's totally disregard this, and this is the ethical dilemma I'm talking about.

So when people try to convince others not to buy pet store animals simply because those animals may harbor health issues/they may cost more with vet bills, it's sidestepping the larger issue. And it also opens up the door for a lot of anecdotal "Well, I bought my dog from a pet store and he's perfectly healthy" arguments. So THAT is my gripe.