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Since GNOME Shell doesn't actually use a desktop anymore, there should not be a ~/Desktop directory by default. As such, it might be better for XDG_DESKTOP_DIR="$HOME/Desktop" to become XDG_DESKTOP_DIR="$HOME" in the default configuration. Not 100% sure if this is a bug that needs to be filed with each Linux distribution or if this should be filed with upstream GNOME (or both)...?
Note that gnome-shell is not the only desktop environment using xdg-user-dirs. Moreover it's not using $HOME either. Also, file management changes are not yet complete and change is coming for gnome 3.2. I also think this is more for a discussion on one of the developers lists on gnome.org, not for this bugzilla. Feel free to open one there.