I went with the auto, not only for ease of driving in city, but it's nice to be able to drop the hammer and just hold on until you lift or see God. There are benefits to the 4L60E when comparing them to the older transmissions. As mentioned, since they are all electronically controlled, shift points, lockup, etc and call be programmed and a paddle shifter setup can be used.
I'm of a different opinion, as I like working the gears on a road course, but with the crazy power/weight ratio of and LSX S30, there isn't really much of a downside to the auto setup. It's purely a personal preference, IMHO.