In other words, despite it looking a lot like GNOME (and admittedly based on GTK+, as even the distributions's developers admit), it's a distribution-specific DE. In that sense, in what way is that any different from Unity (which Canonical was castigated for doing)?
Unity isn't really a full DE like pantheon, at the moment it is mostly just a shell. Ubuntu still technically uses the gnome desktop under the hood (although ubuntu does tend to apply a massive amount of downstream patches to their gnome desktop instead of forking or writing things from scratch).
Unity = A shell that is implemented as a compiz plugin, which ubuntu uses as an alternative to gnome-shell. Ubuntu's desktop = Gnome 3.6 desktop (but without gnome-shell) + tons of ubuntu specific patches + unity shell + some ubuntu specific software (like USC, Ubuntu one, UOA etc...).
Pantheon = A full desktop environment written from scratch using Vala/GTK3, and uses some existing gnome technology like gtk3, gsettings/dconf, libmutter, gvfs etc... (and also some new tech that elementary has developed like Granite, which is an extension of GTK3, and contractor which is a way for apps to communicate with each other).
As you see, ubuntu's desktop implementation is much more...hacky.