The proliferation of permanent, origin-like civics implies that the current origin system is getting overloaded. IIRC, a dev comment about Eager Explorers (or some other permanent, very origin-like civic) explained that it was made a civic rather than an origin because it was desirable that it would not block various origins. Or something like that. IIRC, it was perhaps also around that time that one developer entertained the idea of "society types" (not necessarily an exact quote) as a way of relieving the origin and civic systems of some of their content. But, lacking a link for it, I may misremember. Still, the proliferation of permanent, origin-like civics remains a clear sign that the origin system is (literally) overflowing.
I am open to other and/or more approaches, like the one suggested above in regards to species traits; rolling some origins into species traits certainly seems like a good option, especially if that would be part of making those traits work more consistently between different empires. For instance, most or all homeworld-related origins could be represented as traits that also modify the homeworld of the starting species; this was the case for several species traits in Master of Orion 2, and is technically already the case for the climate preference traits.
- Post-Apocalyptic: the current design can be completely replaced by the Survivor / Radiation Shielding traits and turning the homeworld into a Tomb World.
- Life-Seeded: can be almost completely replaced by adding Gaia climate to the homeworld climate selection, the only things that would be missing are the world size and strategic resource deposits.
- Void Dwellers: this would be trickier, but could still be done - it could be represented as another homeworld "climate" choice, possibly rolling the Void Dweller trait effects into the climate preference trait. There would also need to be some switches for starting technologies and other effects of the origin. This extra effort seems reasonable, given the popularity of the Void Dwellers playstyle and the frequently recurring lamentations that it can't use any other origins.
- Subterranean: the Cave Dweller trait could remain as-is, while the presence of pops with the trait unlocks a planetary decision that gives the effects currently reserved for the origin. This would also finally end the weirdness that happens when subterranean colonies switch owners.
This would leave Doomsday, Remnants, Shattered Ring, and Resource Consolidation as homeworld-themed origins - and the last one or three of them could conceivably also be converted into homeworld or trait options (though I am sceptical about removing Shattered Rings from the origins list). It could arguably be thematically interesting to combine Doomsday with Remnants, Post-Apocalyptic or Calamitous Birth (or even Tree of Life, if that one was converted to a permanent civic or a hypothetical "society type" setting).
Alternatively, with no homeworld-origin-to-trait conversions, the entire homeworld origin column could just be moved to the homeworld selection screen; only Doomsday would need to be kept as an origin (presumably in the Post-FTL column).
Looking at the other origins:
- Necrophage: the trait could be reworked to function regardless of the society they live in.
- It always bothered me that voluntary necrovorism and necrophagophobia are not things in empires without the Necrophage origin; it is as if they cease to be necrophages if they are not ruled by an empire with the Necrophage origin.
- If a population turnover mechanic was introduced (to make the lifespan and xp gain traits matter for pops and not just leaders), the Necrophage trait could tap into that mechanic by growing its pops proportionally to the turnover of other pops (plus any purging and sacrifices taking place). Perhaps also declining if there is too little death around to feed on. They would literally be death-eaters.
- Calamitous Birth: could probably be reworked as a trait that switched the pops' colony ships to the other type, but the effect is still so minor that it could also just be made a feature of the lithoid shipset - which could simultaneously elevate the flavour of lithoids overall (especially if lithoid ships also get reimagined as "lithoid bioships").
- The preset ascension paths (including Clone Army) could have easily been simplified as traits, if only there was not so much content tied to them. I don't have the heart to argue that so much creative work and content should just be thrown out.
- However, something could be said for giving us the option to just pick Limited Cybernetic or Latent Psionic as starting traits, and perhaps also a similar genetic modification predisposition trait ("Epigenes"?), and a lighter version of Pathogenic Genes ("Weak Flesh", negative but unremovable trait?). These traits could simply just exist and, in main species, limit the ascension path picks. Basically, the traits would be "lite" versions of the more elaborate origins, and could then be combined with other origins to achieve the flavour we desire - or be used to lock custom-made AI empires into specific ascension paths (without needing to involve the rest of the origins' content).
- With such traits in place, the ascension-tied origins in the "Evolution" column in the OP could essentially be moved to the "Pre-FTL Society" column, as they would be amplifications of a species trait rather than a separate evolutionary origin (which would now be handled via traits instead).
Looking at some of the current permanent civics:
- Innate Design: it could easily be reimagined as a species trait that prevents modification of that species, unless the trait is removed (while empires with such a main species would presumably not be able/willing to pick any ascension path). The presence of pops with the trait could also unlock (researching) the building currently associated with the civic.
- Storm Devotion: could be flipped so that having pops with the Storm Touched trait unlocks (researching) the buildings, and the Storm Dancer job could then also require the trait.
- Anglers: this civic is not a civic (virtue) per se, but rather about the practical exploitation of a species trait - which the civic currently requires of the main species, but not from species working the jobs added by the Angler civic. An alternative design could be that the presence of Aquatic pops on a wet world unlocks a planetary decision, zone, or other shenanigan that gives the current effects of the civic. And the jobs added should be limited to species with the Aquatic trait.
- Augmentation Bazaars: could be changed from a permanent civic, to being a civic that requires the presence of cybernetic pops (or that the main species is cybernetic). The civic could then be adopted after either picking the Cybernetic Creed origin, picking the Limited Cybernetic starting trait, or choosing cybernetic ascension.
There may be more origins and permanent civics that could be reworked as traits, but Real Life beckons now...
So, in summary:
By moving homeworld origins into traits (or homeworld selection) and adding ascension-oriented species trait picks, the OP's columns for "Homeworld" and "Evolution" could largely be removed. The remaining origins could then be split between two columns, one for pre-FTL societal development and one for post-FTL relations (including Doomsday).