When in window mode, it'd be nice if the graphics display window would come in front of any open menu windows when it's selected. I like to leave menus open so I can select various places to go, but the larger ones block too much of the graphic window.
One can use the Windows shortcut Alt-Tab to cycle among the open windows. Presumably this would bring menu windows to the front as appropriate. Corresponding keyboard shortcuts are available in the various Linux and Unix window managers.