I just went from an '03 RT to a '12 GSA in November. Bob's BMW in MD had two demo bikes - the GS and GSA. I rode the GS, loved it and was ready to buy it. The GS had $4K worth of lights, guards, and other accessories on it which made it more than the GSA. I rode the GSA and bought that instead. I LOVE IT...!
The differences I noted:
RT is better at extended triple digit speeds due to aerodynamics. I usually don't run the GSA above 80, I'm sure the saddle "boxes" cause a lot of drag. It'll probably do a lot better without the bags. I like the wide bars of the GSA better. No more whizzy RT fully linked brakes, yeah! Extended range with GSA tank is nice, don't really notice the extra weight when riding though. No tupperware to deal with when doing maintenance on the GSA. I don't mind getting the GSA filthy on the back roads. The GS and GSA are very confidence-inspiring and forgiving - the swiss army knife of motorcycles in my opinion...