MR2s are great cars, my mom owns a Miata - which we JUST bought a few weeks ago so here is what I remember. Whichever you go with make sure of a few things:
mr2s are non interference motors, if the timing belt goes then it wont hurt anything
miata: miata are intereference motors, if the timing belt goes, it destroys everything. Timing belts on miatas are to be changed ever 75K miles. MAKE SURE THEY HAVE RECIEPTS OF LAST CHANGE!!!!! however, a parts car miata with a good engine can run you only about 500$ where as a parts car mr2 is a lot more money.
in a miata the ECU is stored on the floor of the vehicle. any rust on the floor boards could potentially spell out a bad ECU in your future.
mr2s are more spacious by far than the miata, i'm short (5'1) even in themiata I couldn't really get close enough to the pedals to feel 100% comfortable while driving, a taller person would be comfortable. (I know of miata and mr2 owners over 6')
MR2: body parts are all interchangable from the same generation. 85-89 is interchangable, 91-95 is interchangable, IDK about MKIII.
miata: all body panels are interchangable, 1990-1999 or more. Parts are easy to come by.
convertible top in miata: you can buy a brand new one off of ebay for about 260$ shipped if you get a bad tear. CHECK fOR TEARs. The B pillar in the miata convertible has a tendency to rub on the lining. check this.
miata: stock stereo will not work if you put the wrong security code in 3 times. (it will never work again) they come with a din.5 size stereo, so if you go aftermarket you'll need access to ebay to buy the appropriate dash kit because all the stores that should carry it, don't.
miata vs mr2: storage wise the mr2 is the best way to go, there is more storage room in the trunk, in the inside, and in the front trunk than the miata can offer. miata supports a different sized luggage area though, you could fit a suitcase in the miata where it might be more difficult with the mr2.
miata hardtops sell in various colors for about 400$
if you get a miata, buy a roll bar if it isnt already equipped with one, they sell for about 120$
sound system: I prefer mr2 stock sound system than miata stock sound system. depending what package of miata you choose, there arent speakers in the headrests in all of them (there wasnt in my moms and she has a difficult time hearing her stock stereo while driving)
both cars are a LOT of fun to drive, I really liked how sensitive of steering the miata has, I felt completely in control despite the fact i could barely reach the pedals.
lights behind the dash (gauges) are hard to see at night in the miata.
the side markers freaked me out in the miata at night, but i realized what it was.
they both take regular gas if you prefer.
blue book on both vehicles is incorrect.
i can say i enjoy the miata a lot, i enjoy driving it, convertible is fun too, but at the end of the day i'm glad that i'm getting into my mr2