I have both - a GS and an ST - here's how I see it:
Comfort - hands down it's the GS. You just sit there and do everything. On the freeway the ST has a better ride, however. It's also got a MUCH better flowing windshield. I can take the GS for a ride all day and feel like I've never left. Comfort is a very personal thing. Everyone likes something a little different including the angle that you sit and how much weight you want on the bars. The ST can run all day as well but the GS is a lot more streatched out.
Turns - It's the ST all the way for high speed sweepers. For lower speed and heavy transition speeds (real tight stuff) it's the GS for sure. The GS also rules the bumpy stuff due to the leverage from the wide bars. The ST can be inconsistant at lower speeds over bumps if you weight the bars. Keep the weight off the front end!!! Stay on the gas and, if anything, weight the inside bar. None of this weighting seems to matter on the GS. Just throw it down. The ST likes body language. The GS....whatever makes you happy with the body.
Wind protection - The ST. Much better air flow. The wind shield on the GS simply sucks. This is one of the most talked about windshields on the internet and it's with good reason. The problem is that the windshield is so far away. Lean in and test it. If it were closer to you it would be much better. The GS has a huge benefit with the hand guards when it's below freezing. I know heated hand grips help both models but the hand guards are really noticeable when it's REAL cold. Lower leg warmth is better on the ST when it's cold outside.
Rain - I'd have to give the nod to the GS. Haven't done a huge amount of rain miles on my ST but the GS is very predictable in the rain. I've done nearly 1,000 miles in the rain on my GS. You always feel completely in control. The bike comes back a mess but...riding it's still fun. I always say if it's raining before I go for a ride I'll stay home. If it starts raining after I leave I still finish my ride.
Lights - Some consider it ugly but the headlight on the ST "outshines" any other bike I've ever ridden.
Bags - The GS's, when expanded, are bigger. When they aren't the ST's are larger. The ST bags mount easier.
Center stand - The GS needs to be lifted a foot (just kidding but it's a lot). The ST goes up pulling with one finger.
Power - It's the ST, sorry guys, by a long shot. You will make a pass on the ST without thinking about it. On the GS you may hold back. At the risk of being flamed here's what I read and what I've experienced. The GS dynos at about 84 at the rear wheel (all magazines, both sides of the pond). The magazines that have tested the ST all get about 104 at the rear. That extra power coupled with being MUCH lower makes the ST accelerate much harder at high speeds. I'm talking high speeds here, at lower speeds it's closer than you would think. I've had my GS an indicated 132 and my ST an indicated 145. The GS was done at that speed, the ST MAY have had a little bit more to go. Both are spot on (1 to 2 MPH) according to my GPS at freeway speeds. BTW my GS has some help. A full Remus and an enhanced intake snorkel and air filter. Just had it (the GS) tested last weekend and it pulled 88.78 on a dynojet - about 5 more than all other GS's tested that day (they also had a Remus for the most part).
Living with it - The ST is easier to clean. The back of the GS, even with a hugger, is a mess after riding on a wet road. Go figure!
Engine and gearbox - The ST is smoother and has more consistant fueling - no flat spots. My GS has a noticeable flat spot arount 5,000. The gearbox on the ST is the best I've ever had from a BMW (I've had plenty).
Gas milage - The ST gets 48-50, the GS between 43-45.
Racing - depends on the road. When in doubt take the GS. If I need major power I take my K1200R!!!
Which do I prefer - depends on my mood. That's why I, like so many others, have multiple bikes. Both of these bikes are outstanding for their intended purpose. The GS gets well deserved press for being so versitle and such a great all-round bike. It is. Period, end of story. To me, the ST is the most underated motorcycle on the market today. If you like the riding position you would be shocked at just how well it does.
My 2 cents.