The S2000 is considered rare because it is a low-production car. About 5000 were imported to the U.S. during the first year of production which started mid-1999. Since then, production has been increased with about 7500 being brought to the states every year since 2001.
Honda never intended the S2000 to be a mass produced like an Accord. They are hand assembled, not completely hand built, in Honda's Tochigi plant where the NSX is produced.
There are a few people who say they'd never pay $32K+ for a 4-cylinder 2-seater convertible, when you can get a Miata for about $10K less, but that's not the reason why the S2000 has been declining in sales. The car is just too raw and extreme for many people (not unlike the Elise).
Prior to the makeover a few years into its life cycle, the S2000 was pretty extreme. The ride was teeth-chattering hard, the rear end would snap around if the driver lacked skill, and the engine required high revs (all 9000) to extract its performance. Since the makeover (which included costmetic changes to the front and rear ends in addition to the interior) the ride was softened, the suspension was recalibrated for less oversteer, and the engine was enlarged for more low-end torque (at the cost of a reduced redline). However, the car is still far from being considered a long-haul or commute car.
The Miata is a nice car but I would still choose an S2000 even for $10K more. I'd choose a 911 Carrera S over a Vette any day even though the Vette is about $25K less. Some people don't understand why others pay more for certain cars.
Rumors about the S2000's lifespan have been around since the first year it was available (it was supposedly introduced to celebrate Honda's 50th anniversary). Some of the latest rumors insist that Honda is leaving the sports car market, where they aren't making money, to concentrate on passenger cars and SUVs where they are making tons of money. That makes sense but it's too bad because Honda has made some nice sports cars.
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www.s2ki.com for more info.