My wife went through the same thing recently. She wanted a convertible and likes roadsters. We test drove both a S2000 and a Miata (not MS version). We ended up buying the Miata.
We test drove a 2004 S2000 first. It is fast, handles very well and has better interior/exterior aesthetics (personal opinion of course). However, I found the car incredibly cramped and uncomfortable, it gets worse gas mileage, costs a lot more and costs more to insure.
A couple weeks later, we test drove a 2000 Miata. I wasn't expecting to be impressed having already driven the S2000. However, I was very impressed. The Miata is not near as fast and it may not look near as cool, but it is definitely more satisfying to drive. It is hard to put your finger on exactly what makes the difference. We like the seating position in the Miata better, the transmission feels great, and the car feels extremely nimble. We've taken it on a 200 mile trip and I was not at all uncomfortable. The price difference between the two cars helps a lot as well. On top of that, there is a huge aftermarket of comparatively cheap parts for the Miata. The wife is already asking for forced induction.
I don't know if my opinion will help you make a decision, but good luck.
