I have had the oppurtunity to spend alot of time working on, driving, and riding in, the GT and the GTR. To put it simply, they are two completely different cars. They each have their own characteristics and qualities.
Each car accels in completely different areas. The GTR accelerates and handles better than any car I have ever experienced. With a little bit of computer tuning and a performance exhaust the car literally leaps upon acceleration. I have never experienced anything like it. However, it's not as sexy as the GT and it will never have the mystique or heritage of the GT.
The GT just doesn't handle like an all wheel drive car because it isn't one. At the end of the day the all wheel drive helps ALOT. I think that's something that everyone can agree on.
The GTR is a VERY capable car. On the New Zealand Targa Rally a guy showed up with one that was completely stock. The only work they had done to it was installing a roll cage and racing seats. It still had the stock brake pads in it. The driver finished 5th place overall. We finished 8th in our GT. Now obviously the GT was never built for this type of racing so naturally the GTR would be better suited. I'm just trying to illustrate that each car will perform better in different environments. For example, I would be willing to bet money that a GTR will never beat a GT in a 0-200+ MPH run. Or if you took a GT and a GTR to Daytona (road course) I'd bet that the GT would run away from the GTR. The two cars are COMPLETELY different.
With that being said. If I had the oppurtunity to own one as a second vehicle that I would only take out for weekend trips. I would choose the GT all day long. However, if I could only afford one sports car and it was going to be my daily driver as well as my weekend toy. I would choose the GTR.
Just my opinion...