the boxster is better. You will like it more - for all the various reasons that have already been stated.
When I was shopping for my boxster, I also considered the S2000 and the RX8. I know the RX8 is not a roadster, but i test drove it, and I really really liked the rotary engine, and the sporty way it handled - I rationalized the RX8 as it had back seats and would be a somewaht "practical" 3rd car b/c you could get mor eusage out of it... anyway... of all these three cars...
I liked the boxster the most the boxster was the most fun. the other two cars, were "fun" and I considered them more affordable, more reliable, I could buy a newer one for the same money, etc etc..but in the end, I was buying a third car for me to have fun in - and ultimately, that meant I should buy the car that I really wanted..and what made the little hairs on the back of my next stand up, was the boxster. the way it sounds when you are running toward redline, the way it corners, the way it looks - the S2000, or in your case, the MR2 is a compromise.
Just be prepared that it will cost you more to fix it, and there is a remote possiblity of motor failure that will cost you an arm and a leg. NOt sure what you are looknig to spend, how new/old of a car you are considering if you go the boxster route - but if you have $$$ to spend you can get a CPO car from a dealer and you have no major worries for a while.... if you go the used car route - like I did, you can get a VERY good deal on a base or S model. I would suspect you could find a nice nice nice base model 986 like a 2000-2002 for $10-13k. I bet $15k gets you into a nicely equipped "S" with reasonable miles.
be patient, shop a lot, look at everything, test drive all of them, know WHAT options you want, don't want, and then find one you want and then know that you are in teh driver's seat to to speak as the market for these cars is a buyer's market all the way. have some money stashed to repair stuff that will break.
there is nothing that a good drive in the boxster can't fix.
okay, that's not really true...but you know what I mean.
for me, the S2000 was too small, buzzy, had ZERO low end torque...the boxster was way classier, felt faster (even my base model), and was just an overall better car. in the end, with cars, you usually get what you pay for. look at the MSRP of a new boxster vs a similar year MR2. the Boxster was a $50k car and the MR2 was a $20k-ish car... it's no big suprise the boxster is what you will like more...
arrange to test drive them back to back...on the same day. go home and see which one you still think about when you are back home.... for me, I test drove back to back, and it was obvious which one I wanted...
good luck.