There was some discussion in the "realistic planet population" about factions within an empire.
http://www.freeorion.org/forum/viewtopi ... ht=faction
This also might work as an answer to the question "why do rebellions occur?" in the apty titled "Rebellions!" thread.
http://www.freeorion.org/forum/viewtopi ... ht=faction
Now, I reliaze this has probably been talked about before, but I can't find any obvious discussions.
I'd also like to preface this whole thing by mentioning that I expect this is all far too comlicated for actual inclusion in the (standard) game, but I'm throwing out ideas anyway. It might be moddable or usable to a limited degree. Some internal gamestate representations alluded to here might also be used, which would allow easier extention of the faction system for the more complicated parts of it.
The idea is that factions periodically arise on planets in your empire.
They may be composed of a number of population "points" (or whatever is applicable) and may be generally concentrated on a single planet (initially) and may have a headquarters on that planet (acts as a planet special?).
Natives on a planet, or "foreign nationals" from another empire could be treated as a faction. (This is the part that could be included to allow easier extention)
Perhaps each population point would have attributes such as race and faction affiliation (or just faction afiliation, and foreign nationals are always treated as being in the X foreign nationals faction). (Having a population point affiliated with more than one faction would probably be a bit much...)
Factions have social / military / other agendas (like a SMAC faction) and their happiness / acceptance of empire leadership depends on how these are met. Faction acceptance of empire has effects on the happiness / unrest of the planet where they are located, depending on the portion of the population of the planet that is aligned to the faction. Factions also like / dislike other factions depending on their respective social / military agendas, and occasional nonsensical hatreds (could be explained as racism or planetary nationalism or religious disagreements (reformations, subsects) ). Factions could occasionally split into two subfactions, which would probably be opposed to eachother. Planets with significant numbers of two or more factions could have increase unrest / waste due to faction fighting (gang wars).
Other empires can use spies / money to incite unrest by sponsoring a faction on one of your planets. Their own "foreign nationals" would be particularily succeptible to this.
Particularily unhappy factions that have a large population on a planet could start rebelling. They could ignore imperial orders, form their own militia (ground or light space based), steal imperial ships, start acting like pirates on shipping lanes (if applicable), blow stuff up, or in extreme cases seceed from the empire. Rebelious factions would be particularly vulnerable to enemy spy action... though they could have gotten that way *becase of* enemy spy action.
Colony ships built on a planet may contain primarily members of a certain faction, and the new colony will be affiliated with that faction.
Some factions (religious ones?) have a high tendency to convert people to their faction from a) the general (non faction aligned) populace b) other factions. Aliens / Natives / Foreign Nationals (if treated as a faction) are unlikely to attract new members from your general populace.
Now here's my favourite part: Factions that have been around for some time may also have special bonusus that can offer, like the various specialties of factions in Dune books. This would be very interesting, especially if the standard research tree doesn't offer these possibilities. These 'faction perks' could be quite powerful, much like those in Dune.
The selection of faction perks you have access would probably involve meeting the demands on one faction which upsets another. As such, you would effectively have to choose one or two factions from which to receive perks in your empire. This could be thought of a special general powers in C&C: Generals or picking a particular minor faction to align with in Dune 2000 (or was it Emperor: Battle for Dune?).