What does Stardraw technology involve, exactly? Is it kind of like solar capture technology, but workable for all types of energy? Even so, it seems more sophisticated than that, since the Progenitor can use it to compress the entire universe.
What the heck is a "+ih emitter"? An early prototype of the +ii? What are the differences? Perhaps that's the only version that's flawed...
Endgame spoilers here: Is there any real reason why the emitters suddenly fail after an unknown length of time, other than plot contrivance? It just seems kind of out of the blue. If they can preserve cells for billions of years, why not indefinitely? What causes them to fail?
Why do your crewmates have gender exclusion preferences for whether or not they'll fall in love with Ros? You could say that sexuality is genetic/biological, so they would still have such vestigial traits even if everyone's sterilized...but then why do they have no species preferences in that case? You'd think that that psychological block would be greater, yet it's apparently nonexistent.
It's most likely because the closest equivalent to that would be, for us, preference based on skin colour. Which means that either the creator tried to avoid Fantastic Racism as Unfortunate Implications of characters having such preferences, or they simply hadn't thought of it and thus it's an oversight. Or alternatively, it just might be that specifically for the characters you can romance it happens not to be a big deal at all.
What exactly are the "colonists" at the end of episode 3? Willis says not to have any moral regrets over killing them, because they're "artificial"? What does that mean? Are they robots? Computer programs? But they must be physical in some capacity, since physical weapons can kill them. And they are definitely sentient, since they make the decision to help you in the final mission, something that should be impossibly far outside of their scope if they were programs.
Most certainly subjects of the PLSE experiments - clones of Tezkhra and the many other DNA donors.
Who was that plant merchant?
This blog post seems to hint that it's either #1213 or #0EF7, the two biologists from the abandoned databanks. It's clear from the biology room that plant biology was a branch of their abiogenesis projects, and, if they have access to technology on par with the Progenitor, they fit the "means and resources available" clause. We never meet them in person though, so the hints about speech patterns don't fit with this...
It...could be Willis, maybe? Though we don't ever see him involved in plant biology in particular, as #1213 and #0EF7 were, biology definitely seems to be an interest of his, to the point that he creates an entirely new species, just as #1213 did. As one of EROS' head scientists, he would fit the "means and resources available" clause. We also do get to speak to him, so it would fit the speech pattern recognition clause as well. I'm not sure about the "very specific greeting" part, though...
ThisLet's Play proposes that it's one of the scientist NPCs in the EROS research station, as he's next to the plant exhibit and fits the "very specific greeting" clause.
Why doesn't The Black One participate in the Last Stand against the Horde at the end? He comments on the Heroic Sacrifices, so he was clearly there the whole time. Given that his driving motivation is to prevent the Core from activating, why doesn't he lift a finger to accomplish that? It's also pretty cold of him to leave Neff and the others to die, especially given that he can't be permanently killed and thus wouldn't lose anything in the attempt.