I personally consider this a feature, not a bug. It fits perfectly into my workflow where I always need certain windows open, no matter what workspace I'm on.
To enable workspaces on your second monitor, open gconf-editor and modify the key /desktop/gnome/shell/windows/workspaces_only_on_primary
I believe one of the goals for Gnome 3.4 was to expose more options (such as this one) under System Settings.
Having a setting seems about the best way to handle it. Personally, I prefer the Shell's current default on this. Actually, the Shell was my most pleasant experience with the conventional two headed xrandr setup as a task bar always seemed kind of hokey in this configuration and being able to view all of my windows in an active on screen overview helped keep things organized.
That being said, because I game so much and I actually prefer the two heads to be completely separate, I am currently using Zaphod Mode which makes Gnome 3 hurl. So I am using Xfce for the moment. I would appreciate a similar write up of its features when the next new release comes out by the way Michael.
It appears I missed the press release about this, but when I decided to try gnome shell 3.4 for a short time today, I discovered it now has a dconf setting to disable dynamic workspaces and go back to having a fixed number of workspaces. Under "org.gnome.shell.overrides" there is now a "dynamic-workspaces" dconf key. I needed to reset the dconf key org.gnome.desktop.wm.preferences num-workspaces back to 4 after using it.
Unfortunately, I'm really not keen on how gtk3 programs are now faded when not the current focussed program. It's as if the designers are unable to imagine a scenario where you might want to have more than one program on screen at the same time. I'm not keen on the app menu either. Perhaps by gnome 3.8 someone will sneak in hidden settings to turn those off.