It's unlikely that Paradox would do a very good job clone copying Civ 5 or Galactic Civ 1/2/3, since those games weren't made by Paradox designers and coders. Paradox's work is seen in the game systems of CK II, Victoria 2.
Even if Stellaris borrows concepts from elsewhere, they would still have to design it with their previous work in mind. Even when the subject changes for a studio, their methodology and process, their philosophical thinking, does not, unless one decapitates the leadership and replaces it with a foreign branch.
As for what connects the different population units of aliens together, the various ethos would probably determine how each pop reacts to other pops and situations on planets and in space.
https://forum.paradoxplaza.com/forum/index.php?threads/stellaris-dev-diary-5-empires-and-species.887487/
"Keep in mind, though, that there is a clear difference between the empire you are playing and its founding race. Empires and individual population units ("Pops") have an Ethos, but a species as a whole does not. ...
It is natural for individual Pops to diverge in their Ethics, especially if they do not live in the core region of your empire. This has far reaching consequences for the internal dynamics of empires; how Pops react to your actions, and the creation and management of Factions, etc (more on that in a much later dev diary!) Traits are not as dynamic as ethics, but even they can change (or be changed - this is also something we will speak of more at a later date...)"
If 1 species is to have different ethics and philosophies, one must mechanically be able to see the difference and interact with them, unless Paradox is just making a space box simulator that runs on its own without player input. An abstraction of pop numbers and game mechanics means that the player never has a concrete grasp of it, it is just something made up arbitrarily for one reason or another. A simulation that isn't a black box, doesn't run like that. The rules and outcomes are not arbitrary. It can be changed, unlike a black box. So whether pop is x or y has to depend on concrete player or game mechanics, that is clearly visible.
In a federation, immigration or dealing with occupied populations, would fit the scale of problems Victoria 2 dealt with as well. However, unlike a historical simulation of eras, where one goes from uncivilized to literacy and INdustrial Revolution, a science fiction future has Event Horizons and various other tropes that separate one higher level species from another lower level species. Which Paradox can use as they see fit, when breaking the game up into 3 phases. Exploration/scientific investigation, expansion/empire building, and empire sustainment, internal factions, end game threats.
https://en.wikipedia.org/wiki/Kardashev_scale
There are unique differences in CK2 for playing different cultures and religious mixes, as well as which nation you start with in Victoria 2, due to civilized vs uncivilized vs great power. On the galactic scale, they can also make it very different game play wise, if they go with a stark difference in power and capabilities between Class 1 and Class 3 civilizations.
To make a short comparison, Earth is at .5 to .8 on the Kardashev scale. A civ that can construct and maintain a Dyson sphere or even just a Dyson swarm around a star, would be Class 2. A ring world, would be between Class 1 and 2. Galactic level consciousnesses that can occupy an entire galaxy and vampire kill off all lifeforms on every planet at once, would be closer to a Class 3.
http://store.steampowered.com/app/273070/
As for simulation issues, if they were trying to make a game like that, with unique diplomatic mechanics for each race, they couldn't procedural generate too many random things. But if it is just the ethics and some other variables for a race, like genetics, along with the pops handling most of the load, there should be some naturally occurring mixes. Since a species can randomize their DNA or genetic traits, but that's not going to make more ethos to complicate things. A pop can change their ethos, but not their DNA, barring something tech based.
The difference between Paradox population units and various 4x pop units for me, is that the 4x pop units are more like GUI features, designed to allow the user to micro manage certain game mechanics without using large numbers or big ui icons. In Master of Magic, each worker was about 1000 people, and one can freely change their mode. There was a base limit of how many farmers was needed and the max pop ceiling was around 22-26k so it wasn't that micro intensive. In Victoria 2, the pops are simulated, so how they demote or promote isn't necessarily something you can change at will by using a slider. The 4x game figures are designed to be simplistic, because it's part of the GUI. They expect you to click on it like every 1 to 5 to 10 turns.
As a preference, having played both kinds, Paradox's real time pause with simulation and some sand box elements, but not having roguelike qualities, feels more interesting. It's a better balance of macro with micro management. Although I also thought Master of Orion 3 was great as a war simulator.
