My personal favorites
-The revamped Free Agency process. The pending offers tab, the increased interaction from the player - the entire process is much more involved and fun than ever before
-Much faster PbP resolution and improved PbP text
-The Player Salaries report is almost worth the price of the upgrade alone
-The new shortcut bar at the bottom of the UI. In 2006 I would create a few shortcuts in every new league - the shortcut bar has all of those and more
-FaceGen is an amazing addition for my fictional league
-The early availability of a 2007 MLB roster set.
OK, maybe that last one is wishful thinking.