I've had all three Gens, and have logged over 100K miles in Vipers in the last 10 years.
The simplest comparison I've experienced was at VOI9 driving a stock 2002 RT/10 back to back with a 2006 SRT-10 coupe on the autocross course. The differences were immediate and apparent.
The SRT has more low-end grunt, a smoother-transitioning suspension, and far far better brakes. Keep in mind the '02 has ABS. The '02's ABS activated quite a bit, while the SRT ABS maybe once or twice per run. My overall impression was that the differences felt pretty dramatic.
I've run a couple dozen road course DE events (including 4 Viper Days events) in the past three years with two different Gen II cars (one my current ACR) and a '04 SRT-10. I can't say enough about the Gen 3 brakes. Incredible. Far better than my aftermarket Stop-Tech upgrade on the '00 ACR. I basically matched lap times of the ACR with a bone-stock (down to the paper air filters) SRT-10 (although I have more experience now with the ACR than I did the last time I tracked an SRT-10). The SRT was far less stable over 130 MPH, but the car has no aero stuff like my ACR (wing/splitter).
The GTS is a better-looking car, compared to the SRT-10 convertible, although the SRT convertible is not an ugly car by any means. And the SRT coupe? Great looking car.
Overheating? Never experienced it with any Viper, despite very hard use with all of them. Not even on the track. Even the old 514 stroker Venom Gen 1 car (550 rwhp/580 rear wheel TQ) never ran hot, with a stock radiator.
Bottom line? Stock versus stock, the SRT-10 is a better performer across the board. One of these days, I'll buy a used SRT 'vert with some safety & track mods (including aero!) to use as a track ******.