Here comes the stones, lol.
I've had a 2.5 and now have a 3 with soft tops and in both cars it takes me at least 3 seconds to put the roof down, while still sat in the car and the same to put it up, while still sat in the car. So I wouldnt really call it a pain.
MX5 everytime, besides, the S2000 is considerably more expensive for the same aged, spec'd car