Thinking about it for a while, after reading Barry's wiki column on the subject.
Actually i'd rather have all Applications are to have a icon on the first (primary) Virtual Desktop as well as being accessable via the menu. Having the ability to delete the individual icon on that primary virtal desktop if the user desires of course, but stay in the global menu system for the ability to start that way if so desired. The icon would then open the associated application in a Secondary or later Virtual Desktop with a configuration setting in the desktop setting file.
Or maybe the better idea would be that all the applications should each open an individual virtual desktop for each application when the application was started, basically as if they were each in their own container. But that would depend on raw memory and swapfile availability needs.