I think people conflate being a technically well-trained general surgeon with being a top-notch academic surgeon. I'm making no judgement about whether one is better than another because the surgical world needs both.
Community programs have a very different mission than academic programs. In terms of volume and early operative experience, they, in many cases may have an advantage over many (but by no means all) academic programs. Their mission is to turn out Board-eligible graduates who have the technical and clinical proficiency to safely usher Mrs. Jones through her hemicolectomy/appy/chole/&c.
Obviously, in the current medical environment where the guy who is just a general surgeon and nothing else is becoming as rare as hen's teeth, many community programs are necessarily acquiring fellowship programs and sending their graduates off to fellowships. This is part of a broader (and probably necessary) cultural shift in the practice of surgery.
Academic programs have a different mission. For one, they are usually based in a tertiary care setting which means fewer "bread & butter" cases, often sicker patients requiring complex procedures, and clinical zebras that have been pushed up the referral chain. Second, and this is the main distinction, is the research-setting. They are dedicated to turning out competent surgeons who are also oriented to looking around the bend and advancing the state of the art. A good example is Franny Moore (see this week's excellent New Yorker profile by Atul Gawande), former chairman at the Brigham. He had the curiousity and experimental intuition to conceive elegant methods to revolutionize our understanding of fluids and electrolytes, and the vision to drive transplant medicine to where it is today. Though he was a good surgeon, he wasn't a technically gifted one; it was his steel-trap for a mind and experimental outlook that distinguished him.
While we are all surgeons, community and academic programs are geared to developing very different products. In many cases the community surgeon who does not have research or teaching obligations will be technically far more polished than a Professor of Surgery who is running a tumor immunology lab.
I admit I grow a little impatient with people continually asserting that so-and-so community program turns out surgeons that are just as good, if not better than such-and-such top-five academic program. When it comes to the individual patient lying on the table, of course they do.
For a student applying, you have to decide: "do I love being in the OR, and not need the pain and aggravation of climbing the academic promotion ladder, not being distracted by a lab, and applying for grants" or "do I love being in the OR, but I really want to understand the physiologic and molecular basis of X, and am willing to expend the extra effort to balance this desire with my clinical obligations"?
Or, "am I'm not sure, but I'd really like the opportunity to explore the possibility of doing research"?
I've probably artificially dichotomized the issue somewhat, there are certainly university-based programs that are more community-oriented, but still present some research opportunities. Still, if you really want to pursue research, you want to go to a medical center that has myriad, well-funded opportunities because they'll have the infrastructure (core facilities, track record in securing funding, &c.) to support you.
I think breaking the issue down to just whether you want to pursue fellowship training is actually a small part of the equation nowadays.
