The biggest change: no more +12V voltage support for the new iPod models--essentially no more support for charging through the IEEE-1394 port. Some auto chargers still do work (such as the Griffin AutoPilot), since they charge through the +5V port for USB power.
Riddle me this...I have a 160GB classic that I use a Sik dock cable with at my desk, which has the firewire charging connection, which I'm using with the original firewire AC adapter. How does that match up?