The Gnome 3 default behaviour for Alt-Tab switching displays applications across all virtual desktops and groups together multiple instances of the same application.
If you find this annoying, the list of applications can be limited to the current virtual desktop, using the command:
$ gsettings set org.gnome.shell.app-switcher current-workspace-only true
The setting takes effect immediately and no root access is required!
As for the grouping of multiple instances, these can be cycled through using the <Alt>+` key combination.
With this option enabled, we have however lost the ability to quickly switch to an app running in another virtual desktop. It would be nice if we could use a different key combination, for example <Super>+Tab, to cycle through all virtual desktops. However, currently the <Super>+Tab combination has exactly the same behaviour as <Alt>+Tab. Let me know in the comments if you know of a way to achieve this.