First, I'd like to say I really like this mod, even if I don't have the most updated version yet.
Second, I'd like to say that the Andorians and Vulcans should really not be major races. The reason for that (in my opinion) is that they are part of the Federation. Bajor, while undoubtedly an important player in the DS9 era, is a minor race (correct me if wrong, please). Also, no other Federation race (such as the Tellarites) are a minor race. I can think of three races at least I'd replace them with-
Klingon-Cardassian Alliance: The Alliance of Bajor, Cardassia, and the Klingons from the Mirror Universe. That's just a possibility, though, as they'd need combined ship designs from all those three races and I don't think the ships are unique like the Terran Empire.
The next one was hard..., my first choice was the Kazon from Voyager. They were enemies for at least two seasons, and were a pretty powerful (if completely disorganized) state in that part of the Delta Quadrant. But if you argue that they are also a minor race, than my next choice is quite suprising.
United Federation of Planets (29th Century). The time-travelling, paradox-creating, insane UFP in the future. The guys who intervened in VOY twice, and got into a Temporal Cold War later in Enterprise. I don't know how you could implement Time Travel into this game, but it could be a Super Ability of some sort (Something to do with spies, or maybe... I don't know.) Just a crazy suggestion.