The frame you use will be mostly what you have available and what your personal preference will be. The Fiero is where I have all my experience. I have not had an mr2 or worked on one.
The Fiero can be stretched and reinforced very easily and there is lots of info out on the web on how to do it. Also a large community supporting the Fiero. I have to assume there is lots of support out there for the mr2 as well.
I agree with am33r that the interior and other mechanical items are newer and updated. Fieros did come with A/C and cruise (I have both on my current project) but the cruise is an old vacuum setup which isn't very good. Directions for an easy conversion to an electric cruise control setup is available on the Fiero forum.
The suspension on the Fiero is older and the earlier than '88 models wasn't the best, but again easy ways to fix. Bump steer was the biggest issue with the rear suspension on the Fiero and that can very easily be fixed with an extension outward of the trailing arm mounts on the engine cradle. I removed 95% of my bump steer with an outward placement of the trailing arm mounts. Only time it started to get introduced was near full compression and full extension and if you are that far, you are already in way more trouble than some bump steer.......
These projects usually require wider suspension stances anyway so regardless of whether you have an mr2 or a Fiero, you either widen the suspension or you use massive spacers. My personal preference is to widen the control arms etc. rather than spacers but again, personal preference and there is lots of info out there to do that with a Fiero. Don't know what is available for the mr2.
The stock engine on the mr2 is better than the Fiero but, from what I have seen, there really aren't too many builders that keep the original motors in these projects. A lot of builders end up reorienting the drive train for longitudinal or update the Fiero engine to a V8 etc. The MR2 looks like it might be harder to update the engine but that is only a comment from looking at pictures of the engine bay rather than any experience so just an opinion. Again, I am sure there are many update threads out there for bigger, faster, more powerful drive trains for the mr2 as well.
If you already have a Fiero under the project, take the body off and see how the stretch and reinforcing was done and determine if you are happy with it. If you will need to do updates to the reinforcing etc. to make sure it is safe, you might be better off to start over with a new frame Fiero or mr2 and you can make your call then.
Good luck with the build and looking forward to seeing some pics soon.
Don