The sail was strengthened to withstand under ice operations and improved scopes, SONAR sensors and weapons systems were added. The emphasis was on the new versions of Tomahawk that were hitting the fleet and changes to the proven BSY-2 system were made to enable the newest Los Angeles Class boats to have flawless weapon delivery capability. The newest batches retained the class's current speed and diving depth. New hull coatings gave the boats a stealth-like capabilty.
Funny enough, had I not been medically retired from the Navy, my orders were to the USS San Juan based out of sunny San Diego, California. I didn't put in for them, but as I didn't get the shore duty orders I wanted, I requested a "new construction" boat which is basically you sit in the dock all year (or however long it takes) and then ride the boat once it's built. By that time, three years or so have passed and it's time to start putting in for new orders and this time you can still get shore duty as "NEWCON" counts as "sea duty."
Our kit is the ARII Los Angeles Class sub kit but I used the parts to make her a Flight III boat. Your basic run down is: Flight 1 - basic. Flight 2 - basic but with vertical launch tubes. Flight 3 - vertical launch tubes and no sail planes. The kit builds pretty darn quickly as you can imagine.