I'd think pretty much all of the options should be included there. They could be divided into groups, similarly to how they are in the GUI's panels now. Additionally there could be a group, "playlist", which would of course have all the playlist's settings. Into group "miscellaneous" could be added the track looping setting and skins. Also, perhaps "plugins" wouldn't need a category of its own. 'Auto-load settings' -button and its sub-menu need a place too, and I thought perhaps they could be as a separate item, so as not to be left unnoticed.
Just a simple conception of how it could be done. If someone has a better idea, go right ahead and ignore this