Puzzle games are rigid and limited in scope. So either you go with it on the graphics end with something very simple (as in Tetris) or you go with something more complex and have a mismatch between mechanics and aesthetics. In the latter case you need to get over the hump of learning the rules ASAP. For example, why can't the Sokoban guy pull the boxes? Nobody stops to worry because it's made abundantly clear from the start that this is how it's going to be.
It seems to me like you are judging the game's design from your point of view of how you would make a puzzle game instead of judging it on its own terms.
I think I understand your point of view but let me try to rephrase it first, I'm not sure if this is really where you are coming from:
You think a game like this one, where the presentation is complex, should have had its rules more clear, and that too many of the game's puzzles were difficult not because they were tricky on their own merits, but because their rules were vaguely defined. You need to "think like the game designer", in other words you need to think about the puzzle in some abstract manner instead of as how that puzzle works in the world, as part of the environment. Like, a puzzle should not be abstract and based on arbitrary rules if the game is a realistic-looking trek through a simulated world, it should be things that make sense within that world.
As I understand it, and correct me if I am wrong, you also feel that being unable to complete a puzzle because you do not have all of the information needed to figure it out yet is "unfair" on some level I suppose, or maybe lazy? Again, needing to learn "what the game designer had in mind", its clunky in the same way some old adventure games are, maybe in a similar way a puzzle that requires pixel hunting is, maybe? You should be able to complete any puzzle you are given without the context of the rest of the game, as an independently-made setpiece, with its rules being either self-evident or at least revealed nearby?
I think the game itself is making a very good case for it's approach to puzzle design being valid and worthwhile. I see the value of those guidelines, but I don't see why not following them is a fault, it just seems like the kind of rules that can be broken if done with purpose, something I think this game definitely does.
When I figured out something new and I could now backtrack to some enigmatic door I saw earlier, now armed with new knowledge that would allow me to get through, it felt very satisfying. I was eager to give it a new try. That door which was completely beyond me before was now something I could understand, but even with that understanding, opening it was still a challenge of applying that knowledge in a new way. Given the game's themes of scientific discovery in the audiologs and other things, it seems all pretty appropriate.
You could argue that you feel figuring out those rules is not fun, but then I suppose it comes down to a matter of very subjective opinion, not really something interesting to discuss at length here.