Hopefully Clyde will see this and answer as he's had a lot more Elise seat time than me and he has a miata too.
IIRC the seat was a little lower but not uncomfortable at all, I've been a miata driver since 1994 and when I got in the Elise, both S1 and S2 I dont recall thinking " boy this stinks" or is "different".
It's a pretty good drop when you get into a Miata, but the Elise seemed even a little lower to me. Driving around, I did not really notice that I was any lower than in my Miata, but it was a short test drive and I was rather distracted. Aside from performance, the most noticeable differences were the reduced visibility out the back window in the Elise and that it's harder to get out of the Elise (combination of being a little lower, and the tall, wide door sills that you need to clamber over).
I'm sure that you get used to this. When people ride in my Miata, they invariable comment about how low it is, whereas I'm used to it and take it for granted.
I do have a problem sometimes when I park the Miata next to high curbs. The bottom tip of the car door tends to catch on the sidewalk, particularly after I dump my 170 pounds into the car. Despite being so low, the Elise doors seem to open with a lot of clearance, so I'm hoping this won't be a problem.
I too am a Miata driver, and agree with the posts above. The main difference that I sensed when test-driving the Elise was of being a bit more "enclosed" in the tub formed by the chassis, than the Miata. This must be because the side-rails of the chassis are quite a bit higher than the Miata, but may very well also be because the car and seats are lower. I felt totally comfortable in the car, not at all vulnerable.