The most visible change at the first glanche should be the default color of the Workbench title bar. The WB 2.x is black and the WB 3.x is white.
I miss the nice black bar from my old WB 2.04 (A500 Plus) since i only use 3.1.
The black title bar is down to the older 2.x Kickstarts, not the Workbench version. But I know what you mean....
