Comment 29 for bug 1274740

In normal GNOME session preferences is available in appmenu, no? in GNOME by default that menu is displayed in top panel, but it is possible to change that so this appmenu is displayed by nautilus. At least it was possible in nautilus 3.18 and is still possible in nautilus 3.20.

GNOME Flashback 3.18 has workarounds module that changes Gtk/ShellShowsAppMenu to false. Check System Monitor - there is appmenu button and under that has preferences. Nautilus 3.18 had that too...

If ubuntu will continue to use "GNOME-Flashback:Unity" then for example 0002-Only-use-a-header-bar-in-GNOME-shell.patch must be fixed. It detects GNOME-Flashback as GNOME Shell session:
desktop = g_getenv ("XDG_CURRENT_DESKTOP");
if (desktop && strstr (desktop, "GNOME"))

Then restore-traditional-menu-bar.patch also looks wrong. nautilus-app-menu.ui (Where Preferences is available) is only used when shell shows app menu and shel does not show menubar. I think it should be used also when shell shows app menu is false as it indicate that application should show app menu in window...