UNC gets a ton of NIH funding, not sure if its more than duke or not, and as far as stem cell research goes...I was under the impression that quite a few people are working with them at UNC...atleast thats what ive seen while browsing the website?????
Having thought a lot about this myself, and having been at Duke for more than 5 years now, here's my 2 cents:
Duke is a research powerhouse...UNC is not nearly as much so. When the most recent NIH rankings were released, if I remember correctly Duke is now #3 in terms of NIH research dollars nationally. UNC has been in the top 20 at times, although I'm not sure about their most recent ranking. This too is impressive, but it's a difference in orders of magnitude in terms of the amount of research going on and the people doing it. I'll give you a few examples, to help illustrate my point. The Duke Clinical Research Institute is world-renowned, and is the mecca of cardiology and other sorts of clinical research that has become incredibly important in the practice of modern evidence based medicine. We also have a newly launched and incredibly NIH-funded Translational Medicine Institute, that is headed up by a famous cardiologist who was very nearly named as the new head of the FDA recently. Basic science research is king here too...Duke has a massive grant for AIDS vaccine research, another one for genomics work, and countless individual researchers with lots of grand funding. There are many stories about programs and people like this at Duke. While there are certainly some at UNC as well, this degree of success in research isn't nearly as prevalent, nor are there as many incredible leaders in their respective fields from whom you could learn and with whom you could work (they're generally not ivory tower folks, interestingly...most have been very willing to work with students/residents on research projects here at Duke).
Sure, there's research going on at UNC too, but if your goal is to practice academic medicine and have significant time dedicated towards research during medical school then Duke is really the place to be. That doesn't mean you can't be successful from UNC, but you'll have much less time to do research, and less exposure to the kinds of incredibly successful research mentors that seem to be everywhere you look at Duke. Why not give yourself every advantage possible? Plus, if you're planning to do a residency/fellowship in anything even remotely competitive, it's always best to go to the most reputable program you can, provided you'd be happy there. As much as it may seem unfair or arbitrary, the name makes a big difference in how you're viewed as an applicant...Duke students quite frankly will get more interviews just because they're from Duke.
Here are just a few snippets of what's going on in terms of major research initiatives at Duke:
http://humanvaccine.duke.edu/modules/grant_spt/index.php?id=2 - CHAVI (AIDS vaccine program)
http://www.dtmi.duke.edu/ - Translational Medicine Institute
http://www.dcri.duke.edu/ - Duke Clinical Research Institute
http://genome.duke.edu/ - Institute for Genome Sciences and Policy
http://www.cancer.duke.edu/modules/cancer/index.php?id=4 - Cancer Center research programs
http://www.cancer.duke.edu/modules/news/index.php?storytopic=2 - recent large grants/awards to Cancer Center researchers
