I've owned both a '99 Miata 10th Anniversary Edition with the 6-speed tranny and Bilstien suspension and then an '04 S2000. The Miata was fun, but I hated getting out accelerated by mini-vans. It was pretty much like a go-kart, but just didn't have the straight line "umph". Now, you can buy a cheap Miata and mod the hell out of it. There is a wide assortment of turbo/supercharger kits and everything under the sun for the suspension. I had mine lowered with Ground Control coilovers, KYB AGX shocks and aftermarket sway bars. I have no doubt it could've ripped through a slalom at about 70mph.
The S2000 is in another league though. It's the car the Miata never was and probably never will be. Besides both being RWD roadsters, they really were night and day. The Miata was more euro (MG, Fiat, etc...) whereas the S2000 was pure Japanese, hair on fire, screaming raw performance. It pretty much begged you to redline line it every moment you had. I think out of all the cars I've owned, the S2000 was the most fun, ever. I remember when they came out in 2000 I wanted one so bad, but was in no way financial stable enough to buy one, especially when they were marking them up over $40k (so I got the Miata). But, in 2004, I was able to pick one up for $2,000 under sticker and I went for it. The ONLY reason why I got rid of it last summer was that I needed a commuter that was more practical as my daily driver and neither the Miata nor S2000 are. I did kid myself for years thinking they were fine daily drivers, but I was single, living the bachelor life and wasn't commuting very far back then, so they were perfect. Now it's "married with children". If I could afford to keep 3 cars in the household though, I would have kept the S2000. It's just an unbelievable car. It may be "torqueless" as some people say, but the new AP2's will surprise you. Of course they're not going to feel like a turbocharged car, but the top end is great and the handling isn't too shabby either (better than the MS3).
Honestly, I'd find a used S2000 being sold privately by some old guy that never drove it. Don't waste your money with a certified used. I think the whole certified used program is a scam. It's a Honda man. The engine is pretty much bulletproof and if you get an AP2, the tranny is much better than the older ones that had synchro issues (the new ones have carbon composite synchros). I don't know how much you're willing to spend, but you can probably get an '04 with 40-50k miles for $17-18k. If you can afford 2 cars, go for the S2000. Just realize that it is going to be more expensive to insure and it eats tires like a son-of-a-gun (and you can't rotate - staggered).