They add hormones to meat to make the animals grow up faster. Basically they're growth hormones. That's not something you want to be putting in your body except on purpose. We are supposed to have a balance of hormones since they are pretty much the authorities in our bodies, our chemical messengers that tell other cells what to do. An imbalance can cause health problems in the weakest link in the chain.
They add antibiotics to animals because they are fed a diet that was not designed for them, and they get sick because of it. First of all, you cannot gain health from a sick animal. Secondly, if they consumed antibiotics, then so will you. I can't tell you how many bloggers and threads I've come across where people were justifiably hatin' on the antibiotics. Animal-sourced antibiotics? That can't be good for your own intestinal and gut flora. It's just common sense.
The toxins in these unhealthy animals are stored in the fatty tissues. Because these animals aren't as lean as so-called "paleo animals" (who eat and live like THEIR ancestors), they have extra fat. So basically they have even more room to store even more toxins. It's this whole big thing.
Conventionally-raised animals also lack thier normal levels of fat-soluble vitamins (A,D,E&K), and I see you're already familiar with the omega 3/6 imbalance. There are other factors as well, such as grass-fed beef having CLA which helps you burn fat. But on top of that I also heard a rumor that I haven't actually looked into yet that grass-fed cows/bison can create vitamin K7 which supposedly has amazing health benefits. Huh.
Environmental implications are also present - animals who are allowed to roam freely and feed on grass/natural diet contribute to the cycle of life - factory farms (pretty much where all the other meat comes from!) are very toxic to the environment, creating runoff from chemicals and animal waste and stuff into the rivers and so-on. It's just not good for the Earth.
Also, from the animal-cruelty standpoint, would you really want to eat meat that came at such a cost? The horrors of factory farming should ultimately be discouraged. It truly is a cruel, sad and terrible life for those factory-farmed animals.