I've just spent my lunch break reading the section in the calibre manual on the CLI. The ebook-convert command is truly comprehensive, dealing with all scenarios that are possible in calibre's GUI. Adding an alternative simple GUI to sit on top of all these settings would be a major project, (and basically "re-inventing the wheel"), so I am looking at an alternative method.
I think that it would be possible to use the calibre GUI for all the conversion settings and then use a plugin to:
1) Fetch book/s from user defined source folder and add to calibre.
2) Convert book/s according to settings defined in calibre's GUI.
3) Copy converted book/s to user defined destination location.
4) Delete converted book/s from calibre.
So calibre's folder structure effectively becomes a temporary storage area with all the conversion settings handled by calibre's GUI - which also ensures that any future settings will be covered.