One of the thing I've noticed about playing SK is that with the minor factions, each of them has something unique. You want them to be on your side - or if you conquer them, you get some lucrative resources.
I propose giving each of the minor factions in GC3 something similar - give them some unique power so that they aren't just a one planet pushover and perhaps some incentive to make them your allies (ex: an empire wide bonus or a constant supply of something).
Ideally each of the factions would offer something quite powerful and I would prefer if it were possible if this were XML based (for modders).