I had a 96 cobra, and now I have a 01 GT. I can tell you I miss my cobra like crazy.
The new GT's are GREAT. Much improvments over the previous. But motor to motor the GT will NEVER be as fast as the cobra. With just about every bolt on, I'm still not as fast as most stock LS1's. I run 13.7 @ 101, it's heavy cause of the vert. I know for a fact that with the same bolt ons I'd be running 12's in the cobra.
If you KNOW without a doubt you will get a supercharger, I'd say save the money and get the GT. That's why I didn't get another cobra, but this led to that...... and I never got a supercharger..... and now I'm stuck with a slow car
I wish I just kept my 96 cobra most of the time.
The cobra is more elite, but the GT's are great cars too.