I had an '02 K1200RS for a year, which is basically the same as a K1200GT, so I can probably compare the two.
The pegs are a little higher on the 'Busa, and the bars are lower than on the GT but probably not the RS (the GT has higher risers than the RS). The wind protection on the K-RS/GT is superior but really isn't that great overall (though the RS is better than the GT there, as well) -- if protection is what you're after the RT is probably your bike.
The stock 'Busa seat is loads better than the stock RS seat (known affectionately as a "german torture rack" among the faithful), but I did it one better by switching to a basketweave vinyl corbin front/back seat with backrest (basketweave breathes well in summer and vinyl needs no looking after).
Of course, the 'Busa uses a chain and the K-GT is a shaftie. Since it's a sealed chain, however, it requires little maintenance -- about ten minute's worth after two weeks, five hundred miles, or however far I go on a >500mi day. Chains and sprokets wear out but are easy to replace. When shafts give in some way it ruins your day. BMW shafts do this.
The 'Busa is >150lbs lighter, so it's a bit easier to deal with. The brakes aren't as good (no ABS) as the K-GT's by default but has no power boost to drop out (which happened to me). The 'Busa is more fuel efficient than the K-RS/GT, and since it has a similar tank capacity it has a superior range (that's not saying much considering how far real touring bikes can go).
I have a double-bubble screen which is useful at high speeds in a tuck. I have a ventura rack system and a couple of soft throw-over saddle bags between which I have more carrying capability than my K-RS did with the factory had cases, plus it's a bit more manageable because of how the load is distributed. With panniers and a tank bag you can really go a long way.
Stock suspension on both bikes is pretty so-so. I had to upgrade the one on my K-RS to deal with my weight, but I haven't so far on my 'Busa. If you've grown attached to your in-dash gear indicator, I've also added a generic Acumen model to the 'Busa. I never used the cruise control on the K-RS, though I did notice it was malfunctioning and had the dealer fix it about three times. I put a throttlemeister on the 'Busa and haven't use that either.
I also have SS brake lines and HH pads which stops the bike a great deal better than the stock setup. Also added a jastek "BMW plug" to my left inner fairing, so I can run my heated gear (Gerbing's) with its BMW connector. Replaced the pretty decent headlights with dual HIDs for much improved night driving compared to either stock bike. Throw ALL THIS in, AND a new pipe (should you want one) and some other stuff and you're still spending less than a stock K-RS/GT.
I have made my 'Busa into a decent sport-tourer, at least as good as my K-RS was in all respects except braking, and superior in terms of handling, two-up comfort (my wife really likes the 'Busa more), and balls-to-the-wall-ness. The K-GT does have the better wind protection with the taller shield and extra plastic on the sides, but I don't think that really makes a world of difference -- as I said, real weather protection doesn't show up until an RT or Gold Wing. I ride mine Hayabusa when it's 15degF, anyway.
Hope this helps! Good luck with your decision.