Basically, ships can have a z-axis component to their location as well as an x/y.
Other than the new races, they also added a quasi-3d interface. They also added a few new features not present in the previous game. Sufficient for any fan, at the very least. Overall, I found it enjoyable, if not overly exciting.
I found the storyline sufficiently engaging, though being a Star Trek fan may have had something to do with that. There are ten single player missions for each race for the single player missions.