I bought the car in late 2000, with 85,000km on the odometer (now has just over 144,000km) and from day one I have felt uncomfortable with the rather soft pedal.
I have dríven every model of MX-5, thus of varying mileage, and each one had better brake feel than mine.
In summary:
- changing brake fluid and rating only made a marginal difference
- changing rotors and more "aggressive" pads, made a definite improvement in bite, but not feel.
Still not happy, so I thought I may as well take the final step and change the brake lines themselves.
BINGO!
Even though my OEM lines looked OK, they were obviously "weak" (for lack of a better term).
So for anyone else out there who is unhappy with their brakes, invest in a set of good quality lines and

Thank you to Mr Starlet for helping me with the swap.

[edit 24th Sept]
upon advice for fellow forumites, and years of looking for a good one, I installed a brake master cylinder brace.
In short, yup ..... it works

You don't really feel it under normal/gentle/everyday braking, but if you give the pedal even a half-hearted stomp, you know it's doing it's job.
I assume the harder you brake, the more tangible the feeling.