I believe you could have the best of both worlds. MESS and MAME can be united, yet become even more separated than before.
Why not have C64 or NES be just like any other hardware platform in MAME, that is ROM images you load in MAME just like Pac-Man and Donkey Kong, with their drivers designed in similar manner as any other PCB in MAME, as "driver", not interwoven within and obfuscating MAME code.
Would not that be more natural continuation of the already existing design in MAME? Why not treat C64 "PCB" just like Pacman PCB? Would not this make for cleaner and simpler code, and make both sides equally happy?