I skimmed some of the thread . . .
Magic Engine does play CD games quite well. If using CD "images," they will need to be mounted on a virtual CD drive. It also takes screen shots in the native PCE resolution. Of course, this is from my use of the Windows version. I've never used the Mac version (because I have a real computer, HA!).
As for command lines, I am not a programmer, but I appreciate their use. I love emulators that use command lines because it makes it easier to use with a separate GUI (not the one bundled with the emu). This is great for those who would like to use a single universal GUI for multiple emulators that were programmed by different groups. I've become much more "computer smart" working with command lines BECAUSE of emulators.
I find it laughable that someone could complain about command lines in a FREE program. If you don't like command lines . . . build your own emulator from the ground up with a GUI and show them "how it should be done."