Hmmm. Difficult decision. If price point matters, the Miata wins out hands down. Reliability-wise, hard to say, probably about the same, though the FI on the MS5 means higher maintenance costs long term. The S2000 engine is one of the best built engines in the world. It ships stock with forged crank, forged rods, forged pistons, reinforced aluminum block, and the list goes on. You can FI the S2000 engine to well over 400rwhp with little to no worries without touching the engine internals (however it is costly to FI the S2000). I've driven an S2000, I've not driven an MS5, so I can't really comment there. Stoplight racing between the MS5 and the S2000 you probably won't see much performance difference until the speeds rise above 70MPH at which point I'd say it's all S2000. Same with SCCA racing, since the speeds don't get ridiculous I'd imagine both cars will perform similarly with your average driver, though with a good driver I'd say advantage S2000.
I'd wait until we see the new MS5 come out in 06. That's when I plan to take a test drive in a Miata!