Comment 8 for bug 1267787

Utilities and Sundry come from gnome-shell. gnome-shell uses gnome-menu, which is shared with gnome-panel. The reason they are sparsely populated is because many of the applications in these two categories are not installed by default.

Reverting the gnome-applications.menu is not a solution since it will break the current gnome-shell behaviour (of having utilities and Sundry folders).

gnome-shell 3.12 no longer uses gnome-menus, but presumably gnome-classic would.