Let's set the record straight. The Miata is the better car for a variety of reasons:
-Can be had for the same price or cheaper than a Solid MR2 these days, netting a newer and less rust-prone car.
-Ridiculous aftermarket support.
-Flyin' Miata
-You can not fit an LSx into an MR2.
BUT, despite all that, I've owned 1 NA Miata and 12-14 MR2s.
To appreciate the MR2, you need to be a Toyota enthusiast. They have entertaining handling characteristics from the lower polar moment of inertia and rearward weight bias. They're built like tanks. The 4AGE engine is sweet. I think they represent the pinnacle of Toyota's engineering efforts. I also think they will be historically relevant sooner than the Miata. I wouldn't call them a classic yet, but clean examples are hard to find.
I never had anyone question my lifestyle choices driving an MR2, not that I give a rat's ass either way. If your sensitive or insecure about your manhood, stay away from the Miata.
MR2 evils: Clunky steering over bumps - cheap $2 busing inside the steering rack. This will be needed on every MR2, as they only last about 30k.
Parking brake system is usually shot. New cables and rebuild the rear caliper.
Weak trim pieces:
C-pillar trim on the back. Cracked, or will disintegrate on disassemby and NLA. Someone really needs to reproduce this.
Front lip spoiler and valences. These cars didn't clear curbs/ parking stops when they were stock.
Interior- radio surrounds / cracked dash, ashtray lid
Rust, rust, rust. Cars fall into two camps: Rust-free or rust buckets. There are plenty of rust free cars around if you look outside of the rust belt.
Sorry for rambling. The Miata is the sensible choice. The MR2 is a close second, especially if you appreciate the car on its own merit.