I've always been an MR2 fan, and a Miata fan. And have owned bunches of both. Given the choice and your circumstances, I'd go MR-S. It really is a better driver if you don't need the "large" storage capacity of the Miata, and like the looks ok. The seats are so better as well, and the interior feels more upmarket. The later versions had a limited slip while the earlier ones do not. So if that's important, keep it in mind.
With that out of the way, I'd also shop condition. If the MR-S on the lot is in poor condition, it's not that much superior to the NB to warrant choosing it over the Miata.
They're very close in driver appeal, with the nod going to the MR-S, in my opinion of course.

