I present here an idea I had about using species as basis for new factions. Feel free to read it and comment it. It's not really complete but I thought it would be interesting to share.
It does not presuppose any new mechanic. I think it would be a better option to do something based on cultural identity on a per pop or per planet level but this suggestion would make a good enough replacement with less effort, or at least that's what I feel.
Explanation:
These Species factions represent every species in the Empire (sub-species not differentiated): there are 2 types of species factions.
1-The top 3 to 5 factions in power (see below) are shown in the faction window (the current one or in a new tab)
2-Other species will have "hidden factions", not displayed with very limited events (and as such importance)
These factions have a loyalty measure and a power measure. They also have two favorite ethics.
- Loyalty is computed in function of the species rights. Same species ruler increases loyalty. Temporary modifiers can also change it.
->Having conquered an empire with the faction's species as primary species will decrease the faction loyalty in function of the new pop proportion
The conquest penalty aims to represent separatism.
- Power is computed in function of their relative political power in the empire (at a pop level) and by temporary modifiers.
- Their favorite ethics depend on their pop ethics. Their loyalty changes slightly depending on the loyalty of their favorite ethics' factions.
New factions won't have any events for 5 years.
This would allow the player to avoid surprises and for newly integrated aliens to not cause trouble too soon.
Below are some events that can happen depending on the player's actions and the faction's powers and loyalties and provide some dynamism. They are why you should keep an eye on these factions.
Some of them may need to appear as possibilities in the faction screen, in tooltips or wherever appropriate to tell the player the risks they are taking by antagonizing this faction, for example.
And finally:
That is all. I feel this would make internal politics more alive and separatism a thing, without too much effort. Respectful disagreements and other comments welcome 
It does not presuppose any new mechanic. I think it would be a better option to do something based on cultural identity on a per pop or per planet level but this suggestion would make a good enough replacement with less effort, or at least that's what I feel.
Explanation:
These Species factions represent every species in the Empire (sub-species not differentiated): there are 2 types of species factions.
1-The top 3 to 5 factions in power (see below) are shown in the faction window (the current one or in a new tab)
2-Other species will have "hidden factions", not displayed with very limited events (and as such importance)
These factions have a loyalty measure and a power measure. They also have two favorite ethics.
- Loyalty is computed in function of the species rights. Same species ruler increases loyalty. Temporary modifiers can also change it.
->Having conquered an empire with the faction's species as primary species will decrease the faction loyalty in function of the new pop proportion
The conquest penalty aims to represent separatism.
- Power is computed in function of their relative political power in the empire (at a pop level) and by temporary modifiers.
- Their favorite ethics depend on their pop ethics. Their loyalty changes slightly depending on the loyalty of their favorite ethics' factions.
New factions won't have any events for 5 years.
This would allow the player to avoid surprises and for newly integrated aliens to not cause trouble too soon.
Below are some events that can happen depending on the player's actions and the faction's powers and loyalties and provide some dynamism. They are why you should keep an eye on these factions.
Some of them may need to appear as possibilities in the faction screen, in tooltips or wherever appropriate to tell the player the risks they are taking by antagonizing this faction, for example.
- Ethic faction support
->A random species faction favoring the considered non-xenophobe ethic faction gains power. Pops of this species switches to the faction's ethic. - A skilled leader appears
->Hiring them increases the faction's power - Resist modification project
Trigger if trying to nerve-staple them.
-> "Let's see them try"
- Faction loyalty drops. The event chain "Prepare a coordinated rebellion" will fire if able (see in category "events requiring a low loyalty").
- Project progression is slowed.
-> "Reconsider"
- Maybe this wasn't a good idea: project cancelled.
- Suggest reforms (if one of their favorite factions is xenophobic and some aliens have same rights as them):
They will suggest to lower the rights of said aliens.
->Accepting will grant influence to the empire
- Protest reforms (when lowering their rights, automatically triggered):
Their rights do not actually change as long as the event is not resolved.
->Insist on the change (-50 influence)
->Give up:
-Their species rights do not change - Protest modification project
If the new species template the empire imposes on them has less species points than their current one, this event will automatically trigger.
-> Insist on the change (-50 influence)
->Give up:
- Project is cancelled
- Demand more rights for their species
->refusing will decrease stability on a per planet basis
- Attempt a coup (if the ruler is not a member of their species)
->"They do not stand a chance" (only possible and only option if ruler is the chosen one)
- Their power falls for a decade
->"[Ruler] saw it coming"
(If ruler has "From the Ranks" trait, or was a paranoid scientist, a general, an "Army veteran" or "Oracle" governor,
or a "Cautious" or "Trickster" admiral)
- Their power falls for a decade
->"Fight them with everything we have" (-300 influence)
- Their power falls for a decade
- 25% chance: Ruler dies
->"Surrender" (Stability hit on every planet in function of other species's power)
-Primary species changes to them
-Ethics change to their pop's preference
-Ruler changes
- Resist reforms (when lowering their rights, automatically triggered):
Their rights do not actually change as long as the event is not resolved.
-> Crack down on the dissidents (-50 influence):
-Loyalty further decreased, stability hit on a per planet basis
-> Give up:
-Their species rights do not change
- Improve relations with empires having their species as primary species
- Get intel on empires having their species as influent species
- Appeal to their species to follow empire's ethics (gov. etho attractivity increased)
- Give influence to the empire (amount depending on their own power)
[hidden factions can have this event too]
- Prepare a coordinated rebellion (needs majority in political power in at least 1 planet without martial law):
1 - Will tag every planet with >50% pol. power of that species without martial law
2 - 50% chance of being warned 6 months before it happens, this will always happen if species has no military right
->In that case spending influence allows to stop it, and martial law is declared on tagged planets for 5 years
3 - Every tagged planet create jointly a new vassal empire and instantly declares a war for independance.
- >If species has full military rights, they will get a fleet equivalent to their full naval capacity
>If species has partial military rights, they will get a fleet equivalent to half their naval capacity
>If species has no military rights, they won't have a fleet at start
4 - If nation was a subject and the rebels have at least neutral opinion of the overlord, the overlord will get an event
->Recognizing the rebels allows them to become a subject of the overlord and peace is kept (the other subject won't like that)
->Join the war against the rebels
5 - If a nation with their primary species and similar ethics exists, they will have the opportunity to join the war. If this happens and the war does not end up in their defeat, both nations will fuse into one.
- Give intel to an empire having their species as primary species [hidden event, displayed only to target empire]
- Crime wave:
-> A random planet with >25% political power of that species and more than 10 crime gains the "crime wave" modifier (already exists in-game and adds 30 crime)
And finally:
New edict: "Cultural tolerance" (unlocked by Harmony finisher)
->Loyalty of all species factions increased.
New policy: "Conquest laws" (unlocked by discovering sentient aliens)
->Free and automatic martial law in conquered planets
->No automatic martial law
This would allow to avoid the rebellion event mentioned aboe happening too early without micro or influence cost.
->Loyalty of all species factions increased.
New policy: "Conquest laws" (unlocked by discovering sentient aliens)
->Free and automatic martial law in conquered planets
->No automatic martial law
This would allow to avoid the rebellion event mentioned aboe happening too early without micro or influence cost.
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