Will minor factions be in GC4? I personally didn't like how they were handled in GC3. I feel they serve a purpose for populating the galaxy (the more filled up the galaxy is, the less prone the AI is to rapid expanding, IMO).
Now this brings me to my second point: vassalage. I felt this may have worked in GC3 for absorbing minor civs and other conquered empires into your civilization. It would've been better than the ill-fated commonwealth system (I can see why that was implemented though).
In GC4, if your empire is essentially going to be an "empire of empires", I think this would work out well. And maybe have different options for getting other AIs (big or small) into your empire. Military (either via conquest or "protection" pacts), culture, a quest, etc. Even money: buy small civs outright (everybody has a price for the million dollar man )
Managing and trying to maintain order to an empire filled with a wide array of different mini-civs/factions would be really cool (esp. if some of your assimilated factions hate each other). I was hoping Civ 5/6 would do this (with city states and other conquered civs) but never did. I hope CG4 pulls it off.