As an academy grad, I concur with tscottturner.
Does USUHS give special preference to academy grads? Absolutely. They took in at least 3 people my class year who had difficulty getting in elsewhere.
The academies tend to wean out those they think won't get in anyway. I had a friend with a 26 MCAT but her GPA was 3.4; they wouldn't let her apply since the mins were a 27 MCAT and/or GPA >3.6.
As far as civilian schools, they tend to view service academies well (I interviewed mainly in the south, though). They will let your GPA and/or MCAT slip a bit. Another of my friends had an MCAT of 24 and got into Tulane.
Your biggest foe will be the academy selection board. If they let you apply, you should have a good shot at a civilian school, and if not USUHS should take you. Some schools in particular are Academy friendly: Loyola in Chicago (not to me), Tulane, Georgetown. Private schools seem to like the guaranteed dough. UT San Antonio also has had many grads.
And as tscott noted, if you do your AD first, your chances are even much higher as long as your MCAT is tolerable (>20). This is heresay, but some schools will add points to your GPA if you're an academy grad with active duty experience.
I would recommend doing your AD first if you're really interested in doing some great things in medicine. I wish I had, though I channeled all of my effort on going to directly to med school. So why would I wait now? Your AD commitment is 'only' 5 years. With HPSP, it becomes 9, and with USUHS, 12, and don't forget the intervening 4 years of med school and 3-6 of residency. By the time you finish med school, your perspectives on life, medicine, and the military will change. Things outside of an academy are much different. If you go into med school right after graduation, the military controls you for at least 15 more years. That doesn't include the possibility of being a flight surgeon or doing a fellowship.
Assuming you're a typical academy grad, you're probably more into the hands on fields like surgery, EM, etc. Unless you're in a war zone (Iraq/Afghanistan), the military doesn't utilize these fields well. Surgeons like to operate. Healthy, young soldiers don't need operations (maybe ortho), so you have to find retirees, a VA etc. to get cases. If you're stationed in Korea, good luck.
The big advances and procedures in medicine are in the civilian world. Neurosurgery, transplant surgery, interventional radiology, cardiology, etc. have more action and are easier to get into in the civilian sector. The training (number of patients, cases) is better. There is some evidence that the didactic education in the military is superior (i.e. test scores), but that's due in part to having less patients.
Sure, 5 years of delaying your real dream isn't appetizing. But you can learn a lot, be a part of the 'real' military (docs are very much a support role), and most importantly, totally control your life afterward. If you like the military, you'll have little problem getting into USUHS. If not, your chances are enhanced for civ schools.
