Sometimes, to go forward, you go back. Thing is, the Program Manager was a modal dialogue containing all windows, and could be minimized; you selected program by opening windows containing icons of programs to select. The Gnome Shell eliminates that modal dialogue and moves the icons to an interface off to the side; the current desktop shrinks into the shell's entire display area, allowing you to move to another desktop containing other windows.
In short, windows are brought inside, rather than moved outside, the working space; nothing is behind the working space, but rather, the UI tools move behind the working space when not in use. Instead of icons of windows, Gnome Shell scales the windows down and displays them in a tiled fashion, providing a broad overview of the current working space.
This contrasts with earlier attempts in which the modal dialogue making up the working space was flattened into the background, creating the desktop. All elements of the modal dialogue were scattered around the screen as decoration, and minimized windows appeared in a task bar as titles rather than icons--just as useless when many windows were opened. The step following that was to make multiple working spaces in the same fashion. Gnome Shell has banished most of this, leaving a clock at the top of the screen, but little else to intrude on the use of the work space.