Geographic location has a lot to do with the differences between the school’s admission stats and rankings. Weather is a large part of it. But I think it’s also due to the strength of other schools in its area. Emory is a top-five school in the southeast. Families in Florida, Georgia, Alabama, South Carolina, North Carolina and eastern Tennessee, maybe even Mississippi, looking for a good private school within driving distance have limited choices. There’s Duke, Vandy, Wake, Davidson, then maybe Elon. Public, there’s of course UNC, UF, Clemson, Auburn, GTech, maybe UGa, but those are all huge schools that will be a completely different experience. That’s about it, until you start heading north to Virginia. There just aren’t an abundance of great schools in the south, especially when you get away from the ones with 30,000 students.
Rochester is in a very, very different environment. It competes with way more schools in states with higher population densities where more kids go to college and whose families have money to go to private school. Compare it, for example, to Brandeis, another terrific school which suffers the same way.
You will get comparable educations at both. The quality of the student body will be similar. Both are D-III schools, and in fact are in the same league with other similarly-sized private research schools. Both, too, are highly respected by grad schools and employers.
Chose the one where you’ll be happiest–there’s a high correlation between happiness and performance, although I guess you can debate which causes the other.