Don't discount donor EFI, that being an EFI system, namely ECM and harness from another vehicle, or tuning the OEM ECM.
NISTUNE is available for the RB series of ECM, and seems to be easy to tune. I haven't actually used one (myself), but I have socketed a few ECMs for friends, that do use it. From the limited time I have seen the tuning, it seemed to be pretty intuitive.
I know Apexi also makes a replacement ECM for the RB, I am working on a friend's '71 240Z that he has an RB20DET in, that will be using the Apexi ECU, with boost control add-on.
Personally I use a Delco (General Motors) ECM, with some custom code (public domain) that runs my turbo L28. The ECM I am using was originally used on N/A and turbo I4s and turbo V6s, the code is a modified version of what was used on the turbo V6, though many other variations for N/A, and cylinder counts can be used.
I haven't used a MegaSquirt, because it lacks a few things that I want in an ECM, but with the MS3, it has one of the big ones added in, the VSS, that can make quite the difference in how an engine responds, in my experience with other EFI systems. I plan to get one at some point, mostly for curiosity reasons, than actually using it on anything for a long period.
The nice thing about the donor route is that you know that millions of dollars and many years of research have gone into their development, many have limp home modes, in the event that a major or several minor sensors fail, if a replacement is needed, a call to the local wreckers will usually find you a quick and inexpensive replacement.