The on-field gameplay mechanics will be better, and EA is also steadily building up the off-field options as well. They are adding several new mini-games, such as weird Bowling and Option Dash contests, though it's not clear how these games actually influence Dynasty mode or if they are just meant for a fun diversion.
Obviously, college football is less about individual players and more about the teams. To that end, EA has added a Momentum Meter that can get your whole team more fired up and successful. There's more variation between stadiums as well, so you might see the Florida State Tomahawk Chop or the Florida Gator Chomp.
Graphically, NCAA Football 07 is now quite the stunner. Helmets gleam in the sun, players actually have muscles instead of just flat, low-pixel-count jerseys. There's a new Photo Album mode where you can take pictures of your best moments on the field, and with the improved graphics, there might be a reason to actually use it (and send the files to your 360 friends).