Once again thank you for your support and good ideas! It really helps me to come up with new ideas. I have realized that giving the factions some bonuses and a few extra techs and improvements isn't enough to make them interesting so therefore I have tried to come up with some ideas for them.
The Hive: The Hive have an almost nonexistent culture and is hardly especially tempting to join with. Therefore they should have really weak influence but to prevent their planets from rebelling they have huge Loyalty bonuses (possibly even more than the Yor) from the start and by both tech and improvements. That makes sense since Yang have almost total control over his followers and most of them probably doesn't even know anything about whats happening outside their underground bunkers. This also forces the hive to be really aggressive. But they still need something more than strong loyalty to compensate for their lack of influence since its so important in GC.
Data Angels: In GC you use your spies to gather information about the enemy and cripple their production while in SMAC you could cause revolts, steal tech, make the enemy defect to your faction and so much more. The Angels were all about probe teams (spies) but in GC its a bit harder to make an all espionage faction unless we are talking about a huge espionage bonus. And thats the second problem, everyone who likes micro management raise a hand! Its simply isn't funny to micro manage all the spies. However it could be an interesting faction in the hands of the AI. Imagine an army of spies crippling your industry ruining your ship production and then suddenly the Angel fleet arrive...
Drones: The idea for their military remains the same: lots of low tech units. Domai really cares about his people unlike Yang and has a strong morale bonus. They have the best factories and good influence due to their support for the working class which is the majority of the factions population.
Morgan: Have a penalty in morale due to discontent with the poor because of the large gap between the rich and the poor. Strong trade ability, extra trade route and good economy.
Pirates: Can fully colonize water planets from the start since they are adapted to that environment. Possibly have a slight bonus in planet quality since they can use more of the planet surface (oceans) than the others. They are good shipwrights so they receive a bonus in Military production. However they lack organization and gets a penalty in Economy. I really wish that you could board ships in GC since it really suits the pirates.
Spartans: They are all about the military: Soldiering, weapons, defense and Hp. Ultimately they are supposed to have a fleet consisting of few but very powerful ships. Have the best military in the game but lacks bonuses in the other areas.
University: Research, Research and Research. Well ok, not really but its mostly true for the university. Bonuses in research, creativity and sensors. However because of the lack of ethics they get a morale penalty.
Gaians: Bonus in PQ and cheaper colonization techs. weak soldiering because of their pacifistic tendencies.
Peacekeepers: Strong diplomacy and good morale.
Cyborgs: Strong research although a bit weaker than the University. Low maintenance buildings and weak growth.
Believers: Have good loyalty and morale because of their faith. Good Soldiering because of their fanatic soldiers. Bad research though since they are suspicious to science.
Cult: Really unsure about these guys since they are so tied to the sixth manifold and the whole mind worm mechanism from SMAC
Usurpers: Warriors at heart they get a soldiering bonus and has a bonus in weapons.
Caretakers: Bonus in defense.
Progenitors: +Sensors because of resonance sensitivity. Starts with more techs than the humans. No trade ability instead they rely on a strong economy. A monstrous large loyalty bonus. Why? Because Humans and Progenitors culture, society, technology is too far apart to work for the other. Plus because of the bitter rivalry between the progenitor factions its hardly likely for them to defect to the other. There is a problem however, this doesn't stop them from taking over human planets (perhaps by taking away influence starbases from them?).
I know a lot of the ideas are boring and obvious and even incomplete but most of the "uniqueness" will come from the techs, improvements and components.
Is it possible to alter the starting relations between different civilizations? This way you could simulate the rivalry between the factions.I'm really tired right now and have to sleep but I promise to post some more tomorrow.