Well I know strongly opposing ETHICS will cause wars (Say Goblins find TORTURE ACCEPTABLE but elves find it APPALLING, elves will wage war on goblins based on torture)
A civ made up of creatures that cannot speak will be at war/hostile status due to "not being able to make peace treaties" also two non speaking civs will hate each other for that very reason(I think, haven't done much research in that yet)
All babysnatching civs will be buddies with occasional wars if their ethics conflict (but if have same ethics will remain allies)
all Thief civs will be buddies (same as babysnatchers)
However thieves, babysnatchers, normal, and non speaking/utterances will all be against each other.
so in a way factions can be made
3 factions (Speaking non-babysnatching non theives, Speaking Baby Snatchers, Speaking Theives)
and unlimited? amount of free for all-ers
Trade can be removed if the civ has not PACK animals or WAGON_PULLERS (thus nothing to load merchandise on, no animals to hold, and no animals to pull a wagon)
Having no PROGRESS_TIGGERS or ACTIVE_SEASONs will prevent them from showing up in fortress mode
but if there is a ACTIVE_SEASON just one PROGRESS_TRIGGER above 0 (goes from 0-5) will allow them to show up at that trigger point
Things I want to try, and see if it works is:
Can a layer_linked civ be playable for embark (since layer_linked never actually have wars they won't die out in worldgen)
Can layer_linked civs trade (think this was answered before)
Does a civ that lives farther away from other civs live and prosper more?
those are my only suggestions for your great journey