I always thought that the mechanisms to integrate new pops into your empire are too simplistic. Everyone is unhappy about being conquered for 10 years, and then completely forgets their prior lives once that time period is over. This not only feels wrong, it also makes creating multi-species empires way too easy. To address that, I've put together a model representing acculturation: i.e. how much pops feel like they belong to your nation.
Every sentient pop would gain an attribute called "national identity" (i.e. this excludes drones, robots/droids, and nerve-stapled pops). This would work a little like a pop's ethic: it has a single value (representing which nation that pop feels it belongs to), and has a chance to flip every month. After living in your empire for a sufficiently long period of time, the national identity of xeno pops will convert to the national identity of your nation, unless 1) you are fanatically xenophobe, 2) they are enslaved, or 3) you have a fanatic ethic, and that pop has the exact opposite ethic. On the other hand, if your nation has xenophile ethics and grants citizenship rights to the pops in question, they will culturally assimilate faster. Here's my proposal for the MTTH for each combination of your nation's ethics and the pop's citizenship status. (Assume 1 lifetime = 200 years for immortal pops.)
Fanatical Xenophile + citizenship: 1/2 a lifetime
Xenophile + citizenship: 1 lifetime
Citizenship: 2 lifetimes
Xenophile + residency: 2 lifetimes
Residency: 3 lifetimes
Xenophobe + Residency: 4 lifetimes
Fanatic Xenophobe, or Slavery, or Fanatical opposing ethic: Never
This MTTH would be modified by a few other attributes. A happier pop will assimilate faster, a higher strata pop will assimilate faster, and pops that share your ethos will assimilate faster (and ones that have the opposite ethos will assimilate slower). There should also be a bonus to assimilation time based on the proportion of pops on the planet with your national identity (representing having examples to acculturate to). Conquered pops, and liberated/refugee pops would retain their happiness bonuses/penalties (although those should extend to 1 lifetime, and the conquest penalty should be larger), which should make pops you conquer take longer to assimilate, while pops you save should assimilate faster. Further, there should be a modifier based on the "acceptance" of a pop (i.e. how much that species is seen as being "native" to your nation). That should be a nation-wide value for each species (seen on the species screen) representing how much a species is seen as "belonging" to your nation by pops at large. This would begin at 0, and start to tick up as pops of that species become accultured citizens.
It should also be possible for pops to lose your national identity, particularly if the circumstances are all against them (i.e. wrong ethos, low happiness, low strata, lots of non-national identity pops, xenophobe ethics, etc.) These pops can flip to the national identity of another nation where their species has a high acceptance value, or a "rebel" nation of your species with diametrically opposed ethics.
The proportion of pops with a "foreign" national identity should also feed into separatism. Planets with low happiness and a high proportion of pops that don't have your national identity will want to leave your nation and join the one matching their national identity. The exact proportion needed to break away should depend on your government form (50% for democracies, higher for oligarchies and even higher for imperial/dictatorial); you would get an option to allow this to happen, or try to suppress the separatist movement - which then feeds into an event chain leading to an uprising on that planet. You can of course suppress this with martial law, etc.
Every sentient pop would gain an attribute called "national identity" (i.e. this excludes drones, robots/droids, and nerve-stapled pops). This would work a little like a pop's ethic: it has a single value (representing which nation that pop feels it belongs to), and has a chance to flip every month. After living in your empire for a sufficiently long period of time, the national identity of xeno pops will convert to the national identity of your nation, unless 1) you are fanatically xenophobe, 2) they are enslaved, or 3) you have a fanatic ethic, and that pop has the exact opposite ethic. On the other hand, if your nation has xenophile ethics and grants citizenship rights to the pops in question, they will culturally assimilate faster. Here's my proposal for the MTTH for each combination of your nation's ethics and the pop's citizenship status. (Assume 1 lifetime = 200 years for immortal pops.)
Fanatical Xenophile + citizenship: 1/2 a lifetime
Xenophile + citizenship: 1 lifetime
Citizenship: 2 lifetimes
Xenophile + residency: 2 lifetimes
Residency: 3 lifetimes
Xenophobe + Residency: 4 lifetimes
Fanatic Xenophobe, or Slavery, or Fanatical opposing ethic: Never
This MTTH would be modified by a few other attributes. A happier pop will assimilate faster, a higher strata pop will assimilate faster, and pops that share your ethos will assimilate faster (and ones that have the opposite ethos will assimilate slower). There should also be a bonus to assimilation time based on the proportion of pops on the planet with your national identity (representing having examples to acculturate to). Conquered pops, and liberated/refugee pops would retain their happiness bonuses/penalties (although those should extend to 1 lifetime, and the conquest penalty should be larger), which should make pops you conquer take longer to assimilate, while pops you save should assimilate faster. Further, there should be a modifier based on the "acceptance" of a pop (i.e. how much that species is seen as being "native" to your nation). That should be a nation-wide value for each species (seen on the species screen) representing how much a species is seen as "belonging" to your nation by pops at large. This would begin at 0, and start to tick up as pops of that species become accultured citizens.
It should also be possible for pops to lose your national identity, particularly if the circumstances are all against them (i.e. wrong ethos, low happiness, low strata, lots of non-national identity pops, xenophobe ethics, etc.) These pops can flip to the national identity of another nation where their species has a high acceptance value, or a "rebel" nation of your species with diametrically opposed ethics.
The proportion of pops with a "foreign" national identity should also feed into separatism. Planets with low happiness and a high proportion of pops that don't have your national identity will want to leave your nation and join the one matching their national identity. The exact proportion needed to break away should depend on your government form (50% for democracies, higher for oligarchies and even higher for imperial/dictatorial); you would get an option to allow this to happen, or try to suppress the separatist movement - which then feeds into an event chain leading to an uprising on that planet. You can of course suppress this with martial law, etc.
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