350Z ir a very different animal. I'm not a fan of V6 engines, neither am I a fan of heavy cars, but there's no denying the Z is a capable car. The new ones have 300hp instead of 280 and there are several forced induction kit options. There is one 350Z here that does pretty good in Autocross. 350Z is a GT car - plenty of power for the large and heavy body to go fast, and despite that it handles quite well. Can't carry much speed into the corner, but it's the exit that is more important and all that torque helps.
S2000 is a roadster - lots of grip when You're trying, lots of sideways when You just want to have fun. Not the most powerful car in a 0-60mph race, but will carry more speed in the bends due to a well sorted suspension and lighter weight (than a 350Z). With good tires on a track with lots of tight corners, the 350Z will not be able to put down most of it's power and I can see S2000 clocking up a better laptime.
This scan actually proves my point. On a track like the Nurburgring, the Z is much faster, as there are a lot of high speed sections where the S is left behind. But in Hockenheim (a smaller track with more narrow bends) the lap times are identical.
Then there's the simple pleasure of driving. You can have fun in both cars and "fun" is something that can not be measured simply by looking at the spec sheet. For me, a big and heavy GT car will never be as fun as a small and agile roadster, but that's just me.