Unless you want to consider adding a SC or turbo to your NSX, you cannot compare an NSX to a 996 Pturbo if you are including performance. The Pturbo is just crazy fast right out of the box. Handeling wise, while theyre different neither is really *better*. The AWD of the turbo will loose points amoungst the hardest core, but should gain points for everyone else IMO.
If you exclude performance, IMO, its tough to pick the Porsche. Build quality, cost of ownership, exclusivity, comfort and reliability all tip to the NSX IMO.
The deal breaker for me with the Pturbo is that they're EVERYWHERE. As they should be, they're awesome cars. But, for me, I found that a 02 NSX with a bunch of work (including CTSC) was a much more exciting option than the Pcar. Ive found it reasonably easy to attain Pturbo (996) performance in an NSX and end up with a package that I just like better.