> Correct me if I'm wrong, I thought each system's emulator (like in MAME with > different arcade systems) was different and only the shell of MESS/MAME connected > them up.
You're definitely wrong concerning both MAME and MESS. What you describe is the architecture in Mednafen, not in MAME (and even Mednafen starts to have some more shared components lately)
The actual MAME/MESS structure works as follows: there is a common emulation core (contained in src/emu/) which emulates several CPUs and audio/video/peripheral chips, by using the same infrastructure for them all; then, there are separate 'driver' files (which are the actual per-system emulators, and are contained in src/mame/ or src/mess/) where these common components are connected in the proper way for each emulated system/hardware to work.
Such an approach has a lot of pros (e.g. by sharing emulated components, improvements for a single system, might help many other ones which use the same chips), but does not allow using other emulator sources directly...