My answer would depend
Caveat - I love the S2000. I had a 2001 for a year and sold it for the glass rear window of the 2002.
If your wife really drives hard... S2K. If your wife prefers leisurely driving and a more sedate pace... Z.
IMO, despite the fact that the cars are similarly priced and put up similar stat's they really are two completely different beasts. I'm not saying anything bad about the Z. Its a great value and a lot of car for the money (although I'm not fond of the rear styling) but its a heavy mofo and to me, more of a GT car than a pure sports car.
The S, on the other hand, eschews all but the minimum of comfort for a very pure roadster driving experience. The stereo is only OK at best, the ride is very stiff, you have to really drive the thing to get the most out of it, and its noisy. But I love every second of driving mine and if you (or your wife) put a premium on visceral driving experiences, then look no further.
Also the folks at S2KCA and S2ki.com have been able to verify that the 2004 S2K will have a slightly larger 2.2L motor. Unfortunately, it will also gain a lower redline, softer suspension, and some additional comfort goodies. I doubt that it will be as comfy as the 350Z but Honda appears (at leats in my opinion) to be making the same mistake that Nissan (then Datsun) did with the original Z in that they're watering the car down to be more palatable to a larger audience at the expense of the hardcore driver who really wants the car in the first place.
I hope I'm wrong.