(SPOILERS, obviously. Mostly surface-level.)
I absolutely love the game, but for the sake of discussion, I have to admit that I'm slightly disappointed by the puzzle-paneliness of it all. I didn't read many spoilers over the 8 years of its development, but Jonathan Blow always made a point to emphasize the epiphany-based nature of the game. I took this to mean that as you gain knowledge from the panels, you slowly begin to understand how to use them to engage in more interesting ways with the world. Instead, the opposite is true: the world simply provides different kinds of masks to solve the puzzles with. In other words, the panels are still the beating heart of the game, while the world is mostly static.
To me, this goes against what I like most in games. I find that one of the primary advantages of this interactive medium is the ability to solve puzzles by intuition. Braid was particularly good at this: instead of having to stand in front of a challenge and reason it out in your mind, you could dive right in and play around with the mechanics until your mind took on the solution all on its own. Over time, you acquired a feeling of natural mastery over these new elements. The Witness does not feel like this; more often than not, you have to logic out the puzzles in your head or on paper, and it never feels as good as using the game world to interactively solve a problem.
(Yes, I'm aware of the obelisk puzzles, but it seems they still follow more or less the same formula. But I haven't gotten very far in that direction, so we'll see.)
The game also makes me think about the problem of hidden knowledge in open-world games. Most metroidvania-style games gate the player with keys or abilities, but a few are starting to add paths that are closed solely based on the player's knowledge. One of the first games I remember doing this is Super Metroid: the wall jump and high jump allowed you to get to a lot more places, but they were nearly impossible to discover without the bird helpers. Fez did this with its Tetris language. La-Mulana did it with its obscure inscriptions. And The Witness does it with the ruleset of its various puzzles -- more completely than any other game before it. Still, I wonder if there's a better way to stash away that kind of knowledge. The puzzle panels are a bit too abstract for my tastes. I'd love to see a game where the hidden knowledge you find is entirely ability-based, but not obscure like in Super Metroid.
Again, The Witness is a masterpiece and one of the few games I'd gladly call art. It would be worth $40 just for the opportunity walk around the incredibly beautiful world. Just some food for game design thought! :)