The good news here is that there is no wrong answer. Both have good and bad points. I've 5 Miatas of all flavors, and at least a dozen 1st and 2nd gen MR2s. I personally have a soft spot for the MR2 as it is just more involved in the driving experience than the Miata. Not that I want to slam a Miata, I love them in fact, it's just that in no way shape or form can a Miata feel like a mid engine car, and it has less involving steering feel.
The Miata does have a LOT more aftermarket support, a nicer looking interior, and awesome turn-in, and finding one that's not rusty is easy and the local want ads.
The 1st MR2 has a LOT more room inside, superior steering feel, and one of the best 4cyl motors ever (it's a Cosworth copy after all). It also puts it's power down much better on corner exit, and is more stable under braking on track. Finding a good one is becoming a "search the entire country" activity though.
Really it comes down to which one you like the best, they are so, so different. I don't own either one right now and I have daily withdrawals. I can't find a MR2 patch anywhere to help kick the habit!

