I love this - I am a sucker for cosmic transcendental stuff. There's a couple quirks tho, namely there's entries in the Codex that I am not sure how to unlock (one under World and then another each under each of the people). And the hidden achievements. This needs a wiki <-:
As far as suggestions, the newer improved probes are nice tho I preferred the previous way under some aspects, mostly the fact that it kept spamming the same planet for resources, effectively decuplicating your income... and if I wanted to explore then I could just manually send a single probe to do so. Now probes can trigger the ending, which is not very ideal imo. Maybe consider adding a "only automate X expeditions" so I can set it to, say, 2, and keep using the others manually?
Another thing is that having the automation toggle both under the embers page AND under the probe page is awesome and made me want to have the same toggles also in the motes page and the research page!
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Furthermore, it's explained nowhere that the Hush also increases travel time of probes, took me a while of double checking to verify it.
Lastly, it'd be very nice to have a "cancel expedition" button, maybe available only until 50% of the expedition - clicking it makes the probe return thus spending the same amount of time to come back, so if you cancel after 10s it'll take 10s to come back, cancel at 30 and it takes 30 to come back, and after 50% you can't cancel because there's less time left to come back than it has elapsed. Canceling research could also be interesting.
On a balance level, all civilization research appears basically useless to me, I have always been able to finish building the Ark waaaay before making my way through all green research. Tho not sure what a good solution can be.