Another comment mentioned this but the problem I have with this game is just the lack of information of what ANYTHING does really. I didn't know why there were two nearly identical "clay" resources were until I looked at a storage with the magnifying glass and saw that it said brick storage, I had no idea what bones, bone traps, sculptures, mushroom spores, teno-roots or hearts did or that rain wasn't just a random event until I read the development logs and comments. I STILL have no idea why my guys are exploding, I assume its the "Abominations" but I just can't know for sure because I'm told nothing. You don't even get told when you see a new observation, the first time I opened the Observations button, I had unlocked all but like seven of them because I didn't realize the button was there.
Another example, early on I tried placing wood down, they made a bonfire, "Alright that makes sense" I thought, so I placed more wood down thinking "Wood is surely a building material, it's not just used for fire" and paid the price as I now had three bonfires forming a wall in the middle of the colony and forcing the guys to walk all the way around it, what I learned from this? Each item is going to serve one purpose. Later on, I was struggling to find the last couple observations so I started reading the dev log and that's how I found out seeds have a different effect when placed on land vs on water. That was really frustrating.
I think a book like the other comment suggested would be a really nice way to implement it that just says what items/creatures do/are used for, frame it as a "research journal" since we're supposedly researching the little guys?
This is subjective but you don't need the game to be "mysterious" (Read: inscrutable) to be intriguing, I'm intrigued by the idea an auto-colony sim (that ISN'T ant themed for the thousandth time), I love Worldbox for example, I enjoyed the first half of my playtime here but I only stayed because of sunk cost fallacy and I wanted to finish the last seven entries.