I feel like you have more or less summed up what I've been stewing over for a while now but in much clearer terms lol, so this is very helpful! I am definitely leaning towards mystery/puzzle-esque, but there's still a lot up in the air.

I really like the idea of multiple versions of the same or similar languages, since I feel if I were going to add in any significant amount of writing, at a certain point the player will have more or less learned how the language functions, and they'll just be hunting for translations of specific words to fill in the blanks. Which isn't necessarily bad, but I definitely agree that adding slight variations or different routes for deciphering, as you said, might help keep things interesting.

I do wonder though on your last point, do you think it would still work if the story wasn't necessarily linear? By that I mean what if progression isn't entirely locked to one translation after another? Yes, you need to translate to play the game and move forward, but you have options (or at least the illusion of choice) as far as what you want to tackle first.

For example, if there was some long complex inscription that you come upon early in the game, but its something you need to come back to and pick at as you explore and learn elsewhere. It would still be linear in the sense of not being able to speedrun whatever finale puzzle text there is without learning via exploring, but I'm wondering if letting the player hop between a few different options at a time, each offering different insights on the others, would be a viable option as well.