The biggest differences between CW and GB are location and facilities.
The CW campus is located in Wausau. Wausau is a city of ~40,000 people. The CW campus is located in the hospital (Aspirus Wausau Hospital), but I believe that it uses the anatomy lab of a local technical college (Northcentral Technical College, which is less than 5 minutes away from the hospital campus).
The GB campus is located in the science building of St. Norbert College, a small, private, Catholic, liberal arts college. St. Norbert College is technically located in De Pere, which is right next to Green Bay. MCW-GB has its own classrooms at St. Norbert, and the med students use the college's anatomy lab. (Fun fact: The Packers stay at the St. Norbert dorms during training camp.)
Obviously, Green Bay/De Pere is a much bigger area than Wausau (~130,000 people vs. 40,000 people). Also, Appleton and Oshkosh are approximately 30-45 minutes away from De Pere.
Ultimately, both Wausau and De Pere/Green Bay are very safe areas and are good places to raise kids (if you're at that point in your life). They are both surrounded by small, rural communities and embrace the WI culture. Both cities love beer and the Packers.