This is totally random and out there, but I'm doing another playthrough in preparation for 0.7 and I only just saw a weird detail. Spoilers for anyone who hasn't played through to like 0.3 I guess? Also, yes, this is another ramble from me...
During the dream sequences early on (talking 0.2, right after the study session with Alex), the figure that appears and talks to MC is covered in butterflies. Later on, we get the weird interlude talking about Kredon's Butterflies and their ties to the strange weather.
Just trying to make sense of the weird things going on in the game (Weird in a good way). Caribdis is seeding things, obviously, that hopefully get conclusions by 1.4 (I'm manifesting destiny here since they said between 12 and 14 releases will be had by the end of this journey). The dream sequences are getting stranger and stranger each time I play through, because each time I notice something new (Which considering I've been around since right after 0.2 released and do at least one full playthrough each time an update is released is impressive, kudos Caribdis).
Like, the MC gets the weird phone call urging him to seek Calypso right after arriving in Kredon, then has the first dream of creepy boy before playing Eternum for the first time. Obviously his 100% compatibility is at play somehow, as the Founder acknowledges him right away, Idriel mentions that MC is hopefully the one to finally get it right, and we keep getting these interactions with people (Who I think are NPCs/dead people/enslaved souls) asking if the MC will help them (Important to note, they're not asking him to help them, they're asking if he will, which implies free will matters, same as when Idriel asks the heads or tails question and likes if you break the chain).
We know for a fact that Eternum is able to be modified from Kredon in small ways, Annie mentions you need a lot of skills to modify terrain in your Ion visit, and Nova obviously hacks a way into Ogygia, but that doesn't necessarily mean that Eternum is servers (Thanks Axel for cementing that), but we know it's connected to Earth digitally somehow.
Sort of the last thing I noticed this playthrough is MC's noting that his mom left early on in his life (My brain had it she died before this playthrough), I don't know why but this jumped out at me. What with the 100% compatibility and Calypso's whole heritage thing coming into play for her abilities.
The real last thing, this is straight up just theorizing (A game theory? RIP) but I believe that the founder is the human king from Calypso's legend, the gems of doom are the same as the ones in her story, and the NPCs in the game are people of different worlds. It's noted that they all have a chip in the same place as the neural implant and can be controlled with the new hacker boxes introduced in 0.4, but otherwise go about their lives. Ulysses seems to want to control everything, but the Founder and Idriel (Who I still think is the Elven Queen from Calypso's story, or somehow related at least) want someone who won't. The Gates of Acheron the ten gems of doom open I believe is releasing all the NPCs from Ulysses control, restoring the worlds to their own natural order (possibly sealing them off, which would be reason for Calypso to not be a "main" girl since you can't end with her. Please prove me wrong here, Caribdis).
Actual last thing, still think Hyas should go to Dalia. She's earned it.
EDIT: Found this when you're logging into Eternum to get Calypso... Makes me want to go back through and try to see if there are any other single frame secrets... Good god, Caribdis, can this get any better?