First off, realize that either way you can't go wrong. That said, I will tell you why I went with the GTS:
I like the looks of the GTS more than the RT/10 by a hair. They are both gorgeous machines, but to me the sweeping back glass and subtle spoiler in the back really echo the lines of some classic GT cars such as the Shelby Daytona (obviously). I had also been cautioned about wind noise and the feel of "solidness" on the RT vs. the GTS. Of course, the newer RT's with power windows, etc. have remedied that to my knowledge. There is more room in the GTS, both for storage and in the passenger compartment. The RT with the hard top is just a teeny claustrophobic, as you have that small back glass right behind your head. They say the GTS has a very slight advantage on the track because of the rigid frame and the solid roofline that keeps it in check.
Of course, the RT has one serious advantage over the GTS: Open roof! On a nice summer day, there is no substitute for removing the roof, rolling down the windows (if they have them) and blasting down the road. You feel the wind in your hair (if you have it) and can enjoy the sound of the V-10 as no GTS will ever hear them. While I like the looks of the GTS a bit better, I would say that if I were in a warm climate and didn't regularly track my car, the RT/10 would be very tempting. And I would add stripes, of course.
Either way, you can't go wrong!
Chris