A pre-FTL civilisation would rely largely on long-distance sensors to discover potential worlds for colonization (though of course any data they receive is outdated because it took years for the light to get here), and colonization would have to be done by either suspending the colonists in cryostasis for the duration of the flight, or by using generation ships that just have the crew spawn new generations of colonists until the ship arrives.
The latter also means that ethos drift might occur during the flight since after the original generation dies out, nobody aboard the ship has any memories left of their home world or the original ideals they set out under.
First, broadly to the OP mod direction: I am fascinated by your product and/or service, and wish to subscribe to your newsletter. The rest of this is going to be a breainstorming exercise....
The assumption here is that this is toward a pre-FTL game. Not a pre-spaceflight game. I'd contend that our current civilization, as humans, is effectively pre-spaceflight in that we have no real capability developed to utilize space to benefit us--just a little research maybe, but no ongoing energy or mineral extraction. So, this assumption implies that the player should start with a base higher ability to move things into orbit. If you really wanted to take a step back, then at least make one of the first tech choices be a selection of heavy-lift methods (space elevator, reaction boost, acceleration sling)--that could open interesting events later on....
You have a couple ways to go, but I think keeping things less-fiddly is probably in the spirit of Stellaris. Namely, abstract satellites with tech (they are for science and communication, mainly, or maybe together in a system for offense/defense) and make "space platforms" be where you're putting the meaningful weapons and resource extraction avenues. These are like lesser versions of mining stations and outposts--though the mining/research station itself is simple enough you may not want to mess with it... perhaps just early versions that cost more to build initially and reduce to "base Stellaris cost" as you improve in tech?
You'll want to think carefully about the transition from pre-FTL play to post-FTL play. I think the approach, socially that is, is correct: that prior to FTL the main struggle is around ethos and factions and attempting to create a unified race with which to face the galaxy. While keeping research going and funding enough exploration and settlement to ensure if things blow up you have people left. Once FTL is achieved the faction to which it is associated has a huge advantage, socially speaking. You basically have solved the energy puzzle and can dictate terms to other, less-developed factions. If they don't like those terms--which they might not--then they can steal ships and run away as per a few existing early event chains; you still end up with a unified planet and uniform ethos, quickly.
The player should start with an orbital space station. This would be your spaceport for building ships and essentially have no offense/defense capability in an un-upgraded state. Eventually you would be able to upgrade it into a transition to the base Stellaris station, once you've researched up to a starting weapon tech (and passed through other stages representing its capability growth).
Science development ought to be slow. Very slow. Possibly really only driven in meaningful ways through event-based science breakthroughs and findings. This could be modeled by just making the pathway techs to FTL and base Stellaris equipment very expensive to research. That herds players toward choosing quick wins in sublight tech areas.
On the note of science paths toward FTL, the game should be aware of which ones you've started down, and weigh event discoveries toward that. An easy example could be finding an ancient stargate at the edge of the system--which would still not impart the ability to A) operate it yet, or B) understand how they work, or let alone C) build them.
Here's an idea on how to handle pre-FTL colonization:
1. Build "settlement ships" and "settlement arks". The former are for in-system use. The latter are deep-space vessels.
2. Both provide a single settlement tile on the target planet, the habitability of which should be irrelevant. You can plop a settlement down anywhere, but whether it will thrive is another matter.
3. Once a planet has a settlement (agro, mining or research--all should produce food for 1 pop), it can build additional basic buildings (or more settlements if you want to) on other tiles. Only once a tile is built on can a pop be moved to it. This represents special habitation measures needed.
4. On building a settlement or other pre-FTL building on a tile--whether the first or a subsequent build--two checks should be made: first whether there is a disaster that wipes out a settlement, and second for an event or discovery. This would be where you would get ethos drift in colonist pops, research boosts, alien finds, special energy or ore bonuses, and influence that affects the homeworld.
Note: one of the main ways to get additional growth would be to build more settlement ships/arks and just land more people thereby.
I'm actually not sure if in current Stellaris building a colony ship creates a new pop, or if it is drawn from the homeworld population. Personally I think it should be the latter, but I think it is the former.
You could also do "surveying" of planets by building probe ships and/or expeditions. Which function much like colony ships in that you plop "something" down on a planet tile. This would trigger an event chain that can discover something useful much like settlers do, for that tile. Whether the probe/expedition stays behind on the tile is up to you--if yes, then that could be useful as a "known" event trigger should you get a settlement on the planet later and upgrade that tile to a real building. (It would also prevent just spamming a single tile for new events, which is immersion-breaking.) Think pre-positioned resources (so to speak), plus data collected but not transmitted, observations on long-term environment effects, etc. Obviously a probe or expedition's failure and/or success could have a significant effect on the homeworld factions/pops.
Basically the game would function as a kind of lite Victoria 2-in-Spaaaaace. Which would be terribly cool. (I'd like to imagine, BTW, that you might be able to achieve a kind of Space 1889 feel with some of the tech/decisions.)
If the homeworld is all or mostly destroyed in a disaster (nuclear war, asteroid, biological plague, zombies, extra-dimension invasion of angels/demons [apocalypse], financial meltdown, luddite revolution, core drilling, moon breaks in half, etc. etc.) then you have a couple scenarios:
1. A few tiles survive the destruction with pops on them. Then you can rebuild and carry on. Possibly treating the pops as if they were settling their own homeworld, and let them make discoveries as they clear tiles and build new buildings--after all, not everything was trashed, right?
2. No pops survive. The planet can be flagged for discovery when surveyed: maybe there are scattered groups that could be reconstituted into a pop should the homeworld be re-colonized [event]? Maybe a research project opens to understand what happened and glean lessons/technology from it? Maybe there are active remnants of hazardous influences on the planet? Maybe whatever creatures are alive down there are now sufficiently different that they represent a new civilization in the Stellaris sense of natives? Maybe whatever creatures are alive down there are now no more than hostile environment hazards (giant radioactive lizards, zombies, demons, dangerous robots, intelligent apes, etc.)?
3. No pops survive and you have no pops off-planet. Game over. Your civilization's demise will serve to instruct another.
On planetary buildings: players should not start with administrative centers/capitals in the Stellaris use of the building. Better to have metropolitan zones, which can be upgraded to administrative centers. The tech to do so would be an important step toward planetary centralization.
Enough for now.
Edit: Nevermind, ok more: a good way you could model a civil war would simply be to "land" faction military forces on the planet and let it duke it out with the presumptive ruling group's forces. Whether or not this includes limited use of mass-destruction weapons could be based on the faction ethos, pop ethos and the policies set. I don't know if it's possible to change the name of policies dynamically during gameplay, but you could treat "orbital bombardment" as a proxy for "WMD application". Which WMD could be based on techs developed.
If you cannot change policy names dynamically, then a separate section of pre-FTL policies should probably be provided (and then hidden later?). These policies should be a significant lever with which to nudge the people toward full unification.
--Khanwulf