The autos have a few differences such as smaller turbo housing, and different cams among other small differences. If you like having more control I would say go with a manual, I am happy with my auto, but it just isn't as fun. Although in heavy traffic I love having an auto.
"hmm...not much differ.....HOLY CRAP!" - Unluky (MO) In response to a question about the difference from stock to Stage III.