There's are some huge differences no one has discussed yet: cost, alumni network, community connections, academic offerings, and campus atmosphere. Full disclosure: I work for the university, but in a totally different college. Nothing to do with the health sciences side. I'm a GRU alum, but I started college in the Macon area. Have tried both, and GRU/Augusta is the clear winner.
Cost. Mercer is a small, expensive, private school. GRU is a public Research I institution. Granted, OP is a high achieving student. So he/she has probably been given a full ride. But if not, the cost-conscious choice is GRU.
Alumni network. Mercer is smaller (8,000 students). GRU is bigger (12,000 students). It's not a huge difference, but there are more GRU grads with whom to network.
Community connections. GRU has 56 clinical medical practice sites, alone, across the state. Not to mention partnerships in dentistry, nursing, allied health sciences, art, music, education... the list goes on. GRU for the win.
Campus atmosphere. Macon is a pile of poo. SERIOUSLY. Augusta is awesome. Home of the Masters tournament and world-class golf courses. Kayaking the Savannah River. Running/biking the Canal towpath. Some of the best fishing and hunting in the U.S. (if you're into that). World championship disc golfing. First Friday and the arts community. Sky City and the awesome bands that come through. Amazing food downtown. A hundred festivals every year. A huge international community. Clear choice here is GRU and Augusta. All the culture of Atlanta, none of the traffic. (I'm originally from Atlanta)
Career trajectory. Fun fact: EVERY freshman thinks he or she will be a doctor. Then they get to A&P and burn out. OP is smart. He/she will do well. But the options as to what to do at Mercer are much more limited. GRU is a comprehensive research I institution. If he/she burns out of med school - or simply decides that something else is more exciting (some students think they want to be doctors, but find they really prefer something more hands-on, like dentistry; or they don't want the malpractice insurance costs, and go with a P.A. or N.A. certification, instead; or they decide that the amazing research GRU is producing is totally their bag) - then GRU offers him/her more choices as to how to switch gears.