I recently traded my 2nd Miata on a 2005 S2000. I thought I'd miss the Miata, I was wrong. Don't misunderstand, I loved my Miata, but the S2000 is just that much more car. The new engine is very drivable, great MPG, more usable trunk. I usually run out of speed limit before running out of gears, and still get 28 miles/gallon.
Looks (I have Suzuka Blue and have never seen another like it), transmission, handling, MPG
The boot cover design stinks on ice. Simply moving the snaps toward the center of the car a few inches would make it much easier to install. I actually went so far as to make my own slip on cover out of black fabric to keep out the dust on the commute to and from work.