I have a 2007 R1200GS as well as my 2006 K1200GT. Two complete opposite ends of the biking spectrum. I love both and would miss either.
* The GS is very easy to swing a leg over, start and run around town, I feel the GT is like taxiing out a Lear Jet in comparison for a run to the grocery store. I think the GS is over 100 lbs lighter...
* The GS is made for ease of maintenance, and the GT, well, is hard to do anything but change the oil and final drivve fluid for most "normal" people...
* I did an Iron Butt last year on the GS, and the trip would have been WAY MORE comfortable on the GT- and faster too! Very little protection on the GS from wind, rain, etc.
* The GS is fairly a common site on the road. The GT still seems pretty rare,at least in my part of the country. Both have a different but great curb appeal.
Basically, if I want a very "care free" ride, I'll take the GS. If I'm interested in a little more "excitement', I'll take the GT. I think the GS is much easier to deal with in tight, stop and go traffic, the GT was made for stretching it's legs on the freeway.