The Z3/Z4 is a different kind of sports car than the Miata/S2000 kind. It's heavier which required a stronger/heavier engine to maintain Miata-like power-to-weight. The suspension is softer and, due to the car's heavier weight, less nimble. It's closer to GT car than sports car.
Interesting you would argue the Z3 was heavier when the Boxster (986) was only 100 kg lighter than the Z3 M roadster and the Z3 was basically the same as the Boxster. I've never driven a Boxster or Cayman, however, so I can't comment much further than that.
Not that there's anything wrong with the entry-level ones. It'd be incredibly fun to own a flat six Cayman, and they sell so cheaply used that I wonder why they aren't more popular.
The Z3 is an interesting comparison. Inexpensiveness was part of the British formula that Mazda preserved, and it's not present with something like a Z3. I guess whether you regard that as important is a question of taste, or politics.
I was responding mostly to the absolute statement "best two seater sports car ever made". I think the Miata is a great car, probably the best intro sports car if you are into grassroots racing or similar hobbyist activities, but I'd take the Z3 over it for most purposes.
But they really aren't in the same class. Z3's are tourers, not sports cars per se'. But then again, MX-5's are roadsters, not sports cars in the practical sense. They don't exist in the same market bracket and fulfil entirely different ownership purposes :)
My personal opinion however, after finally settling on a NA mx-5 for my weekend race car, is that the mx-5 is honestly one of the best bang-for-buck circuit cars you can get. With only ~$10k invested in mine, it happily outpaces cars 6-10x the value.
The trouble with this sort of thing is, if you're going to remove practicality and low cost from the equation when making your "best sports car" assessment, you're competing against every sports car ever made by Ferrari, Porsche, Jaguar, etc. on their own terms. Pretty much all the reasons why you'd say a Z3 is a better sports car than, say, a Jaguar E-Type involve practicality and cost, I would think.
The BMW Z3 would like to have a word. (I was actually going to say the 911, but not being super familiar I had to look it up and it does have a rear seat. Who knew?)
But Mazda has always been a great innovator, especially for the cost. They are the last enthusiast car brand available for the average buyer.