Well, still wondering what they were smoking when they decided the "Three houses controlling territory" idea was good for release.
One, unified SPQR controlled by the Senate or a Despot, and that's it.
Yeah, the player should have control over the all faction, while the senate would influence the strategy, what faction to invade or make peace with,... and the generals would be rewarded or punished accordingly. If any general went against the will of the senate, then it could cause a civil war, with the game allowing the player to decide which faction to side with. And depending on the power of said general, he could take over rome and become emperor - full control of the empire. The senate would then become more of a cloak and dagger organization, providing assistance or trouble(assassination/bribery...), depending on how the player handles them.