Ok, looks like I am 11 years late to this conversation, but I personally really enjoy the Acura NSX S S Zero as featured in GT2 et al. Properly tuned, it's one of several NSX models that can "do it all'. As far as the "best" NSX, as some here have already suggested, the answer depends on a combination of utility (your specific ad hoc driving needs for a given track or series) and personal preferences including "feel", style, and many other factors from speed to aesthetics to handling to, well, you name it. In my experience, every NSX I've experienced so far has been a righteous ride, sometimes right out of the box (stock) but add-ons and tuning always help. When I finally, during my current GT2 play-through in which I'm finally taking the time to explore a wide range of vehicles in-depth, forced myself to try the active brake stabilization control (due to the massive spin-out potential of several new-to-me so-called MR cars which were more accurately RR given the engine placement making the distribution worse than 65-35 like all TVRs I own because they seemed amazing on paper + many other RR & some MR vehicles), it transformed my GT world, making several formerly "twitchy" cars - whose great love in life seemed to be allowing me to experience 720s and worse at the slightest provocation lol - into much more stable and dare I say even enjoyable vehicles with great potential. And yes, eventually I added active brake control to my NSX which honestly made it far more stable and a consistently reliable rival-killer under a much wider variety of race conditions. In short, every NSX I've taken the time to get to really know in GT has proven worthwhile to say the least especially when (much) time was taken to modify, tune, test and re-modify/adjust tuning as needed on each vehicle and IMO, the NSX is one of the better (not-too-hard-to-acquire) "all-around" cars in GT.
In my current game I went from a '93 Honda sedan to an Impreza WRX STI VI to an Acura NSX S Zero and then discovered some amazing cars I'd never tried b4, won many I'd also never acquired, and discovered several astoundingly great "rare" used variants of certain models I'd favored in the past + many new-to-me makes and models all of which which is a delight.
I feel that I should express my appreciation for the great information posted by GT Planet members including practical advice, useful data presented in various formats including lists of every type, endless opinions and back-and-forth dialogues and a lot of good humor, high-spirits, and a clear "love of the game" & enthusiasm in terms of both Polyphony's GT series and automobile culture, style, the driving experience and engineering etc including everything from full-blown dragsters, bad-a-s rally cars, wicked world-class road racers and formula cars to compacts, kei cars and even karts and everything in-between.
Forgive my enthusiasm-driven pontification bordering on pedantry. But wow, this latest very in-depth play-though after a long break has opened my eyes to the true depth of Gran Turismo and wow, it's pretty incredible. Again, your posts have proven useful and are often humorous so a big thank you to everyone who contributed to the plethora of useful information here.
And yes, I digressed wildly and can but humbly request your forgiveness for my mad zeal. Long story short: All the NSXs are the best one, depending on your specific driving needs and/or style and "feel" preferences, at least in my limited experience having only played up to GT 5. Every version has it's good points including musical choices and cars included and I love how the list of vehicles keeps growing by leaps and bounds with each release, the graphics revolution over the past 20 years which has gone from the semi-pixelated GT 1 to the photo-realistic GT 6 and 7. I was so pleased with the graphics from GT 3 and 4 but Polyphony continues to set new benchmarks not just in terms of graphics but also music and number of cars/tracks and pretty much in every other way as well although I have read of certain negative re: the GTs I haven't yet played like GT 6 and GT 7.
In any case, amazing game, and yeah, go with the NSX that pleases you the most overall. The '91, '94, '97, type S Zero et all are all nice choices but you have many other wonderful options to choose from as well so have fun spending endless hours acquiring then tinkering with multiple NSX models from Acura and Honda alike.