This is always such a fun discussion.
I found the quad 4 engines by GM in an article one time and just fell in love with the looks and the power so I proceeded to build my Locost around it. I bought a bell housing from Quad 4 rods, $450, a T5 tranny from a 6 cyl Camaro. about $600 after the rebuild, and a rear end from a 79 Supra live axel, posi track and disk brakes, and the right width. Going the many part route certainly causes a few problems to work out, but then that's why I was doing the project in the first place. I will say that solving all the problems, which wasn't all that hard most of the time, did eat up a certain amount of time. I started the project thinking I'd finish in a year or so and almost 10 years later I finally got it licensed. I did take 2 1/2 years off on another project. The single donor Miata would seem to be about the best, easy sort of, and quickest choice. But it's all kind of an emotional thing anyway, more than logical.
I love my Quad 4 it fits in the chassis really well with out having to build new headers or anything. sounds wonderful, runs really strong, and draws a lot of attention at a car show.
I'm personally always drawn to the unusual for some reason. So I probably wouldn't build with a Miata or a Toyota just because they're more common. But I'm not knocking either. find something that speaks to you.