SC works on low RPM's while Turbo starts to kick in at higher rpm's wich makes it more logical to get a SC to get better acceleration ( to me) and you'll keep the warranty.. but hell the S/C won't fit on a GTS anyway
atleast not the TRD
first off, read and research about forced induction before you post about it.
a supercharger will yield a smooth powerband, but less top end power. however, a Turbo system can be customized to whatever your needs are. if you want quick acceleration down low and are not worried about top end power, get a smaller Turbo. for more top end power, go for larger Turbos. if you're looking for top end power while maintaining no lag, study compression maps and see which Turbocharger suits your application.
im doing a custom setup using a t3 super 60 Turbo, which isn't TOO big, but still spools up pretty fast(2k rpms). the only reason i would see to get the supercharger is for preference or if you are a TRD
freak(at least if you have a GT), because for 3.5K you could have a Turbo which would yield lots of power(both tq and hp all over the powerband).