I'm a wee bit late on this, having only just seen it, but thought I would share my thoughts:
Personally I would rather buy from local and independent shops, but having had to move back with my parents I don't really get a chance to do that any more. They use 3 of the giants often, one of which I wouldn't ever shop at if I had a choice purely because of ethical reasons.
Having lost my job early this year because our small Deli was out competed by Tescos, Lidl and Aldie all in the same small countryside town, I would always tend to want to support small businesses now. When I lived in Northwich, we had a fantastic butcher who stocked completely local, free range meats, and you know what? They were actually cheaper than Sainsbury's up the road, and the quality was 10 x better.
The odd thing about living in North Wales, which as you can imagine is a very farming orientated area, is that it is ridiculously difficult to find any locally source meat anywhere! What is the sense in that? I think a lot of it comes down to the absurd amount of giant supermarkets we have despite being a very rural area, where the nearest city is well over an hour away. People just aren't interested in buying local stuff because they think they can get it cheaper in the bigger shops.
Obviously there are good points to supermarkets, the jobs being the most important one I can think of right now.
All in all, the main cons that make me want to avoid them are a.) out competing small businesses, and b.) I hate how unethical a lot of the meat is. Aside from how manufactured a lot of it is, I wouldn't want to touch certain things with a barge pole (battery farmed chickens, pork from the EU, veal, etc). And I often find that supermarket meat is tasteless, oily and shrinks when cooked (yay for pumping water into meat!)
Saying that, there are some that I do like, mainly because their ethical policies are better. Sainsbury's, Morrisons, Waitrose, etc. If I had any of those locally then I would be more willing to shop at a supermarket.
Hope any of that made sense or helped in anyway :3