A couple questions I'm having trouble finding the answers too....
When you join a faction, are you stuck in that faction for the remaining life of the game? In other words if the game goes to 2050 AD will I be in the faction for the entire time?
Why aren't there factions for the non-government civics? Why not a beauracratic faction, or an organized religion faction?
As to the first question, I have been told that factions are expected to disolve and return under a new banner quite often as new government civics are researched. Which would free you I guess to move to a new faction, however, you cannot leave said faction until after their term is up, and you can only be in one faction at a time. (I'm sure some of the more wisened veterans can further clarify?)
As to the second question, I think that's more of what's in a given faction's platform, and additionally, the public decided to have "penalty" civics which a given government civic could not adopt, which lead to factions being centered around various government civics.
Right now, the only government civic available is Despotism.
I envision new factions down the road as new civics become available.
There are also guilds, who act like lobyists, as Croxis put it, to pursuade the factions in their choices, among which would be their factions platform on non-government factions.
Since my head is starting to hurt a bit, I'll leave that fertilizer on the ground, in hopes that someone plants better seeds than mine.