Based on the original poster's question and the fact that he is even considering a GT, I'm going to make the assumption that he is more interested in 1/4 mile performance than handling ability/interior/etc. If that is the case, yes... stock for stock the S2000 will stomp the GT.

But if you want to have a "drag car" DO NOT buy an S2000. The would be a complete misuse of the car, and pretty much stupid. You could dump five thousand dollars in the GT and it would be FAR beyond what the S2000 is realistically capable of without forced induction.