After digging through a lot of the files and solving a majority of the puzzles, I can confidently say that I think the characters are a super strong aspect of the game, backed up by (in my opinion) phenomenal world building in the case of the level 4 logs.
Kari and Nanami are by far the most interesting characters to me, and I would *LOVE* to see them get fleshed out and see where their routes go.
While the main quests are a bit lacking, this is to be expected, but how the characters behave and respond to things feels good and seeing how they each handle the situations keeps me engaged. I absolutely encourage you to flesh out the story and the characters.
I think the main reason you see a lot of people talking about the puzzles is that they are probably seen an avenue to advance the story, which is why I think its a tad odd that you can do the story without interacting with the puzzles at all. Even just thinking of the suggestion of making them more intertwined seems like a nightmarish rabbit hole in terms of development, but I think what we have now is solid enough to be expanded upon in the current system.