I see a lot of potential in the system, but as is I agree it's awkward.
1. Generic units- this is interesting because from my understanding of the interface, it would technically be possible to say, get your rangers to level 1 purity upgrade, and then go 12 points into say, harmony, and max them out with a harmony buff instead of the second purity buff. I say technically because realistically, if you somehow went 12/12 in purity and harmony and DIDN'T win, you're doing it wrong.
I get that hybrids should be rare(or maybe it's just impossible anyways and that's a graphical holdover), but the extra ability to customize your units more(one of the strongest potential features) is very interesting, and I wish the "offshoot" branches were scaled down. This is especially odd when they seem to flat out acknowledge that you might want to go "wide" with the unique units, who have easy to access hybrids. I really think the final "tier" of units should require 12 or whatever in your main path, and then something like 6 or 7 in the other two(whatever the difference is from the main, plus maybe a little more to make it slightly harder).
2. You seem to get affinity from tech/quests/virtues, in that order of frequency/importance. In game actions mattering would help, but so would just having quest rewards give specific amounts of affinity points. Murdering the siege worm shouldn't just be a flat econ bonus, that everyone does, but instead should wind up giving purity points, or maybe only even appear if you're so far down the purity path. Harmony players might instead somehow try to mess with them in other ways, or get points for getting a nest in their borders(and that whole mechanic, along with aliens themselves has tons of potential that NEEDS to be explored rather than left as is. Each affinity should interact with them VERY differently. Not "as needed the exact same").
Purity players should get affinity points for building terrascapes, and supremacy for...i dunno...mag railing the earth? Ok so maybe that's not so great, but you get the idea. Allow us more avenues to really express/reinforce the culture and actually FEEL like that's the choice we made. Maybe even make things that harm your affinity level in one and boost in another. They'll give good bonuses, but harm hybrid players. Civ has always under explored the "in game actions" bonuses. Like the bonus for discovering the world was round in Civ 5 giving bonus embarked movement. Great idea, and rewards certain playstyles while flavorful as hell, and giving the player an idea of something they might want to do. More of that should exist.
3. Military being related to paths is VERY interesting, and has again, tons of potential, but right now is just too binary and strange. It limits tech choices/options and hinders growth in an awkward way. This would be somewhat absolved if there were, again, other ways to get affinity points(or important amounts) besides techs, rather than forcing the "you need X amount of affinity to not die to Y player". Also i'll just add, the starting forces NEED to be better. It's silly how weak the initial units are(maybe this is a personal player skill thing, but is there ANY reason to start with a soldier? It's so weak and useless that by the time you're ready to do anything with it, you could've gotten any other bonus and been far enough ahead to afford a soldier.)
4. Balance in general. Wonders need to matter(and should relate more to their affinities. I'd love MUCH stronger wonders that can only be built at 10 purity or 8 harmony or whatever), the orbital system is begging for more real use(there's like 4 interesting ones, and most of them relate to combat. The economic side is woefully unexplored until late game). Just...a whole bunch of stuff. If they at least tweak the balance first(arguably easier than the other overhauls) it'll help a lot with how constricting the game feels(hello trade routes).
Honestly, the game scares me in some ways, because I see some really great stuff coming from this, and i'm worried as hell that since this isn't "Civ 6" it's not going to get the polish it might actually deserve(even though I do think it could've launched with a HELL of a lot more, and i'm not going to be happy if they charge for the first batch of polish).