Bill,
That's a tough question for me to answer objectively. Athens CC is classic Ross and I've really enjoyed the few times I've played there. I would say Athens CC is more of a shot maker's course because you need to work the ball more and the greens have some great features, typical Ross. UGA is a bigger course, longer, wider, more topography. I do think the new green designs at UGA, along with some of the other strategic changes made in the recent renovation have added to the overall shot value of the course.
If I had to choose one to play, for me it would be UGA because of all the experiences I've had there. I bet the majority would pick Athens CC because it's Ross and the playing conditions (greens) are usually better. As for the golf team continuing to play at Athens CC through the years, my understanding was that it had a lot to do with pace of play, overall course conditions, and better scoring potential. UGA has always been a difficult course to consistently score well on, partially for the reasons above.
I should add that UGA has come along way with playing conditions and I know now that they are working very hard on any remaining pace of play issues (probably no more than 4.5 hours on their busiest days). The course is in really good shape tee to green and the new greens are good, although they will certainly benefit from the upcoming cooler temps. this fall.
John