People have suggested there be more factions in this game, I agree, but instead of the matches turning into Dark Matter vs Rebs or IMPs vs SC ect, how about the other factions be a supportive/attacker encounter faction that the IMP and REB player gets to use.
In Battle Fleet Gothic there was lots of random chance encounters involving a random non-majority fleet jumping into the battle. When the enter the battle it can be from any point on the table, even some times next to the players fleet even if your three rounds in.
How it would play is this other factions ships would be controlled by both players durning there movement and attack phase. In this game it could have it so each phase only one player gets to use the third faction. Or the forces r split and used by both players at the same time, it can not agttack its own forces however. Hell depending on the misdion you could have lots more than three factions fighting.
They could make all the other factions ships be carded bases OR they could use models. I hope for the 2nd option because Dark Sun and ZC have lots of very awesome looking craft.