You're not going to like my answer, probably, but it's what I believe.
I'm a DO surgery resident, and compared a couple of programs on my path to getting where I am. Des Peres (St.Louis) and Olympia Fields (Chicago) and where I am now, Southpointe Hospital, Cleveland.
I believe that after the 5 years of training, at the end, you will have what you need to get going in general surgery, plus have enough opportunity to get fellowship if you want it, pretty much no matter where you go. They all have their strengths and weaknesses, i.e, at Olympia Fields at the time I was looking at it, their residents did NO endoscopy, but they are a trauma center. My program gives you plenty of endoscopy experience by the end (which, from what I gather, is important according to job ads) but has no trauma (we go out for our trauma rotations). My choice had a lot to do with location and the fact that my roots/life are in the Cleveland area.
I was always leary of "newer" programs, and stayed away from those with really bad reputations (i.e, Peninsula in NY--although I've heard they're getting better). Our program has had its rough spots, but we have a program director who cares about our education and our experience. I know there could be many improvements in the way things are done, but again, that's anywhere. I'll still be well-trained at the end. We get to rotate at the Cleveland Clinic, too.