It's quite incredible that Gnome 3.0 was almost an identical mess as KDE 4.0 had been a year or two earlier. Both are much better now, more stable, but both also still have their issues, and don't feel like a real improvement over Gnome 2.0 or KDE 3.5.
Now the main file manager for Gnome 3.0, Nautilus has buttons with nearly identical icons that mean vastly different things, one is a menu, the other is a list view. Also it does not integrate with other desktops well from a look and feel perpective, here is a screenshot under XFCE (KDE would not look better).The push for window buttons inside the toolbar makes for a funny looking window. In Gnome Shell, it's not much better, plus there are some windows with a dark theme and some with a standard theme all mixed together.
On the left is Caja: an updated GTK 2.0 version of Nautilus. I find it more functional, I don't really understand the push to remove most options from the screen in Gnome 3.0. The only positive thing I can see on for the new Nautilus, is the grey color for the left side, which looks more readable and polished.
Interestingly, Nautilus within Ubuntu Unity feels better, it has a real menu and standard looking window. I suppose they customized it quite a bit.