I heard about problems described in this bug report in Ubuntu 13.10, but when I updated from Ubuntu 13.04 to 13.10 I did't noticed any issues with setting custom layout switching shortcut (alt+shift or ctrl+shift) in System Settings -> Text Enty, so I can confirm that it already fixed in gnome-control-settings.
I heard about problems described in this bug report in Ubuntu 13.10, but when I updated from Ubuntu 13.04 to 13.10 I did't noticed any issues with setting custom layout switching shortcut (alt+shift or ctrl+shift) in System Settings -> Text Enty, so I can confirm that it already fixed in gnome-control- settings.