The one glaring difference is the abolishment of an auction style bidding system in which companies bid for placement in the search engines. Some businesses are already complaining because of the lack of transparency. In the existing Yahoo system (as well as Google), customers could bid just one cent more to appear higher in the search engines. Not knowing what others are paying for keywords takes this advantage away, potentially creating more revenue for Yahoo.
However, the lack of transparency may drive advertisers away. We shall see. Yahoo's new system is set to launch in the 4th quarter or in the first quarter 2007. Given, the long delays already, I'd put my money on the first quarter at the earliest.
YHOO-GOOG 1-yr comparison chart: