I hope this thread isn't viewed as bashing the Mac OS X port of PCSX2, because I mean to do anything but that - I'm just a curious fellow who doesn't understand anything about coding or running emulators. :]

Why does PCSX2 have to run through the X11 program? Is it in the application's future to run as its own... Thing?

Because the gui is based on gtk, which is not osx native, zerogs(graphics plugin) also uses X11 opengl extensions, zeropad is based on x11 functions mostly. Theoretically, zzogl might go away from using x11 in the future, and the new gui is cross-platform, so it might run using quartz sometime