In addition to the new ship types, the book contained rules for modular Starfortresses (in space and on the ground) and for Captive Towed Tactical Missiles (CAPTACs). It also offered a special damage chart for when a ship gets reduced to 20% of its starting strength.
Unfortunately, since I acquired my copy via an online minis purchase, I don't have the entire ruleset--just pages 3-10 from the middle of the book. A look over at the Starfleet Wars Book 2 entry on BoardGameGeek.com, however, reveals there are rules for damage control as well as details about the Starfortress modules, including life support, communications, and, of course weapons.
Of particular interest to obsessives like myself is the fact that the second book changes the stats for the Entomalian Mantis-class Galactic Dreadnought. I recently learned from the Galactic Knights Yahoo Group that the original Mantis was cast in multiple pieces with two separate turrets; the replacement was a single-piece model. I'm guessing the reason for the change was economical, and had to do with the logistics of casting a three-piece mini vs. a single-piece model.
Although I haven't read the entire rulebook, it looks like Book 2 was a good effort in rounding out the game and providing game stats for the additional models available.