The main difference is the 3rd Generation has Bluetooth 2.1 + EDR and the 2nd Generation does not. Also the battery for music Playback on 3 Generation is 30 hours max and the 2nd Generation is listed as 36 hours playback time. Most likely due to the absence of Bluetooth.
Ref: http://support.apple.com/kb/SP496 2nd Generation
http://support.apple.com/kb/SP571 3rd Generation
And according to the www.ifixit.com web site the LCD Screens are different.