What you are talking about is simply making pj64 plugins completely unrelevant to GC/Wii emulation, they can't be shared between the emus
Specs: intel i5 3570k @ 3.4GHz;
16Gb RAM; Raedon HD 7900;
Win8 64-Bit
16Gb RAM; Raedon HD 7900;
Win8 64-Bit

Maybe we can even make dolphin connect to the emulated GBAs for linking support thats all integrated. Seeing as they all seem to work together integrated GBA emulation would rock and shouldnt be "TOO" difficult seeing as the GBA hardware is pretty simple. Maybe we could even combine with some other open source GBA emulator into one unified GC/wii/tri/GB/GBC/GBA/DS emulator. We could even rename dolphin to like "nintendo is the shit" or NITS. then N64 snes and NES would be cool just for goos measure but the GBA would actually add a massive usability boost to dolphin. On a personal note that might keep dolphin being developed for a lot longer unlike all the freaking 64 emulators that havent been developed for since like 2007.