I was given an explanation that I feel covers the subject nicely. At this point, the authors wish to focus on having the best n64 emulator for low end machines that is possible. This means that they emulate the core of the n64 and the other systems as well as possible. Creating a UI that allows you to play those games is part of that, but adding complex subroutines to do auto-plugin or game specific plugin settings would be adding a layer of complexity that would result in slower work on the primary goals of 1964.
Since I sense arguement brewing already, let me put it this way...
.85 was released thanksgiving of last year.
I hear this question a lot. nobody took the freely available source of .85, and added this feature, in almost a year now. If you really want it, code it.