I've actually lived in both cities and to me, Atlanta is the better city. Considering that you're coming from San Francisco, you would probably have a much easier transition moving from San Francisco to Atlanta.
Atlanta has more to offer in terms of housing, shopping, amenities, entertainment, culture and it has better schools in the suburbs. Alpharetta, GA is north of the city and it boasts some excellent schools (if you have children) as well as a very high quality of life. There are many people from California that live in the Alpharetta area
and much like Atlanta, you won't find a shortage of things to there as well.
Austin is not as big overall, but I found out that during my time of living there, there were many people that came from big cities like yourself who had a very hard time adapting to the city and they eventually left after a few years. If your a big professional sports fan, you won't like it at all, because Austin has no pro sports teams from any major leagues. While there is no state taxes, property taxes are ridiculously high. My dad lives north of the city in Georgetown, TX and his property taxes are $15,000 a year on a $550,000 home. Austin does lack culture compared to most other major cities all across the country and the weather over there can be hot about 6-9 months out of the year. Austin does have its share of restaurants and parks, but it's not necessarily shoppers paradise out there either.
I'd choose Atlanta over Austin, because of the fact that there are more things to do out there and you would have many more different choices as far as being able to find housing.
P.S. Live in Phoenix currently and I absolutely love it.