Spitballing some tweaks I'd make to the game for balancing reasons. These aren't really suggestions, more musings, which is why I'm posting them here and not anywhere it might be taken as official feedback.
First: Remove the 12 civics win state entirely. It forces a certain kind of gameplay that doesn't always mesh with the stories being told in the Mission Trees (since each Faction has specific methods of integration that don't always fit the paths you can go down) and isn't especially well-balanced anyway (looking at you, Federation). Make the win entirely about who has the most points, which can be gained through many, many different types of play-styles, including civic-grabbing if you like. I'd also open up all options to integrate civics to all Factions, with penalties if you use a style that doesn't match your current Faction's values, possibly to the extent of even locking you out of Missions down a branch entirely if you really break character. Like if you wage an occupation war right out the gate with the Federation. You can do it, but it's going to make things difficult for you.
Second: Some tweaks to the Mission Tree. As it stands, it feels a little awkward to me and not well-integrated to gameplay, so since all the Mission Trees basically only have two routes right now, I'd lean into that more. Give each Faction a starting, mutually exclusive choice. NOT a choice that makes the branches exclusive just yet, but a choice that blatantly favors one side or the other and makes going down the opposite route a little less optimal. This should give you an idea of the tone of your game, and make it more obvious that you have goals to work for.
Now for the factions. This isn't going to be 100% lore-accurate, but then neither is the game. I'm fudging things to give all factions a rough equivalent starting point.
Cardassians: Cardassian starting planets should be extremely resource thin, have a ton of blockers, almost no boosts, whatever. Each planet only have one or two Agriculture districts, a handful of mines, maybe some all right energy production, but that's it. Have all the slots be city districts. The point is that having Bajor already occupied should be a huge deal. Make it the only resource-heavy planet in reach.
The reason for this would be to make it really hard to decide to let it go, which is where the Mission Tree comes in. For the Cardassians their "starting choice" would be choosing to assimilate Bajor or not. Choosing to assimilate gives major boosts to Forced Labor that are only useful if you go down the canon side of the tree (since slavery gets abolished on the other side) and choosing NOT to gives somewhat more mediocre but more universal boosts to, say, Diplomacy or a one-time Unity/Influence boost (or just removes penalties for Diplomatic integration), but at the expense of permanently removing the option of assimilating Bajor. Picking one or the other maybe unlocks the entirety of the rest of the tree so you can start progressing. This is also why you'd need to remove the 12 civic win state.
Taking the option to assimilate Bajor should feel easier, because it is. That's why Cardassia did it. Choosing not to should be a struggle that only pays off in the long run, if you make it that long. Whichever you pick should have an impact to your early gameplay.
Romulans: Have the Romulans start after the star has exploded, not before. They start with a ruined economy and maybe some temporary population penalties. Since their tree seems to be "xenophobic or nay" have their starting options be whether or not they reach out for help (form 2 diplomatic pacts with another Power or something, something easy) or retreat to lick their own wounds and start obsessively re-building in anticipation of attack. I'm less sure what rewards for each node should be, but I was thinking: Retreating should probably boost defensive stats, either for Fleet power or in counter-propaganda or something, maybe some small, permanent resource buffs, and give Unity at the expense of a permanent Diplomacy debuff and having to take a longer early game growth period, while reaching out for help should give a good amount of starting resources (but no buff) and some Influence, at the expense of long-term self-sufficiency benefits and a slower military growth speed. Both should give the same decent Espionage boost.
Federation: Not many changes here, but for balance's sake (and to give a more immediate reason to choose one path or another) have the Federation start after encountering the Borg for the first time, maybe. Their science ships are toast, their Fleet is WRECKED, and their officers in the negatives right off the bat (but recovering). The decision for the Federation is whether they choose to start drastic militarization in response to this threat or if they take a more moderate approach in fear of losing the core of their Federation. Choosing the "Militarize" node should give massive boosts to officer production and ship building at the expense of a major Diplomacy debuff and fewer Science Leaders, and staying true should slightly boost Diplomacy, give more Science Leaders, and maybe some Unity in return for a debuff to ship building speed and much, much higher resource requirements for officer-producing buildings. Funding can only go to so many places, so the idea is that whichever you choose to fund has the easy road while you need to scrape and save to build up whatever it is you chose not to fund. Maybe both options change what sort of tech you can research right away (not remove options entirely, but shift the likelihood a bit), if they ever get around to actually weighting those randomized tech branches. Again, this choice wouldn't lock you out of either branch yet, but it should make choosing the opposite branch a struggle.
Slightly off topic, but I thought about removing penalties for choosing to engage in an occupation war if you hit the militarize node, but chose not to. I feel that would have to be THE choice that locks you out of the canon path later. The point of no return, if you will.
Klingons: Less sure about the Klingons, but I'd say no debuffs to start for these guys. The Klingon choice comes down to what you decide to do when you're surrounded by weakened neighbors. Do you choose to conquer or assist? Do you feel like you must take these civilizations under your wing for their own protection, all under the Klingon banner alone, or do you wish to help them back to full strength first, and along the way perhaps find an...ally? I feel like the rewards should be pretty clear. The only twist I might add is that going down the Assist path eventually gives a Unity buff/a buff to all resources gained/something like that while at war if you go to war with a power that is at least Equivilant to your own. Now that they are back to full strength, perhaps it is time for glorious battle?
