As to slaughterhouses? There is nothing wrong with slaughterhouses.
There is in having a near-total oligopoly of it such that even agriculture heavy states have one or two giant slaughterhouses and everything is legally required to go through them. One of the few exemptions is religious slaughter, and often kosher and halal slaughtered meat is of higher quality.
As to bakeries? Yeah, shit sucks, bro. In theory Panera sells "fresh baked" bread but who knows how true that is.
Bread is so easy to make yourself that while I usually have a loaf of the goyshit around for sandwiches, if I want a real bread I'll make it myself. The flour/water/salt/yeast no-knead variety is pretty much what Panera makes, although generally better.
As for other stuff, both Whole Foods and Trader Joe's have good cheese selections (avoid WF when a TJ item will be comparable in quality and much lower in price), and I can order the rest off Amazon. As for produce, a farmer's market takes care of that.
And when I want some unusual meat (like pork belly which for some reason is ridiculous to get except in bulk), again, there's Amazon, or ordering it directly from somewhere. And I know a couple fishers and hunters who bag way more than they need and give it out as gifts. Fresh caught crappie is great for a fry.
Unless you live in some absolute ghetto shithole with no or useless public transportation and nothing but liquor stores and ghetto groceries where all the food's expired (and maybe you shouldn't have burned down that nice store you used to have in a chimp rage), it's entirely possible to have great food.
Bread, you can make yourself or find a bakery. Whole Foods actually has excellent choices, and local bakeries still exist most places. Cheese is so easily transportable that you can get it from anywhere in the world. I'd put our produce up against anywhere in the world with a few exceptions like tomatoes you ordinarily get in a grocery store or Wal-Mart are absolutely inedible and shit, and you should get them locally instead.
As for meat, the main problem is the bottleneck of a tiny number of slaughterhouses having an oligopoly over virtually the entire supply unless you hunt, know someone who does, or get kosher or halal meats or other rare exceptions to the oligopoly. So if the one or two slaughterhouses in your state don't make a cut, fuck you. You can now get meme cuts like tri-tip and tomahawk nearly anywhere, but short of buying shares in a cow, you're not getting it exactly the way you want if you want something not offered.
That said, nearly anything USDA Prime or Choice is worth the price and however fucked up and bureaucratic USDA is, their quality control is pretty top-notch. Also number of mad cow cases in the U.S. Zero. Nuff said.