This has already been asked, and refused, but I don't understand why.
1964 saves the last set of plugins for the next time you run it.
It would be nice if it associated a plugin setup to a given ROM.
When you close a ROM in 1964 and open another, 1964 could associate the current plugin set to the ROM you just closed. Or maybe add an option "associate the current set of plugin to the ROM" in the gui (better option IMO). Then the next time you load that ROM, 1964 automatically pics up the plugin setup that one has associated. If there is no specific plugin setup associated, or if a plugin is missing, 1964 colud fall back on the default set of plugins...
This would be convenient, for the users, and I don't think it would require tons of work on your side.
You could store this information in a ini file (but not in the main ini, because this kind of settings is very configuration dependant...)