[doug_porsche]

I have owned both.

I think the S2000 gets an unfair rap in that…
If you drive both cars Conservative, (imagine a non-car enthusiastically driver), and shift before 4500-5000 RPM, you will find they driver very similar.
The unfair rap that the S2000 gets is the Mr Hyde that comes out to play at around 6000 RPM.
The “Normal” driver will say both cars drive “Nice”
The more performance orientated driver will say, “they pull similar until the Vtec engages, then its party time in the Honda!”

In fareness, I had the gen 2 S2k with BIG 2.2 ltr motor which help side step the low end torque issue.

Plus for the Miata.
Stone dead reliable.
WYSIWYG car. Very fiew supprises with a Miata. (A HUGE complement to Mazada designers here) HVAC controls are dead simple to under stand, and the HVAC works without any supprises. Glove box is exactly where you would assume the glove box would be. The ride will not beat you to death (but if you modify it you are still a threat at the local autocross). The gas pedle makes the car go faster, the break pedle make the car go slower, the shifter is a delight.
Unless you are very rediculas with speed, they are stealth, hmm, or so I have been told because I never exceed the posted speed limit!
Great aftermarket (remarkably simple bolt in and boom, you have a Chevy LS motor in your stock looking miata)

Plus for the S2000
Honda reliablity.
Bit classier interior, but does hold some (plesant) supprizes (the hidden glovebox, for example)
More unique car. You will see multiple Miata’s a day (again a tribute to their success), you MAY see 1 S2000 a day.
The Shifter is amazing (frequently voted, back in its day, as one of the indistries 10 best production shifters)
Power top. fast to go up and down. Nice day, I am at a red light, lets go topless!

Only has a couple of down sides with the Honda.
I found I rarely had to turn the AC down. Mine tended to blow cool, not cold, air. May have just needed a recharge.
I drove a Lotus Elise. With the exception of getting into and out of the car, the Lotus was just more of an event to drive. (and by event I mean the little angle on your shoulder seems to be asthmatic and the little devil on your other shoulder bough a megaphone!)

Summary. There is no wrong choice. Buy the newest, best condition, version of either car and you will not be disappointed.