I know have 9 cubes, 3 keys and I've found a bell which I'm sure there is a system behind ringing but I've just plundered on. Here's a pic of the door I found that shows only at night. (Sorry quality is crap)
Started a new game and now I can look about in first person. I did a puzzle that involved me looking behind a boiler. I tried to do the chair ones where the codes are obscured but couldn't get it to go through. I did a fair bit of walking about testing out the new first person stuff and didn't really like it.
I went through a few rooms I didn't work out the first time and didn't fare any better this time around.
I think I need to make the sea drop to progress. The pyramid which I couldn't figure out earlier in the game has a door in front of it with loads of cubes on, which I can see because of a glitch with the first person stuff.
I'm a bit annoyed the new game + didn't make all the spoken legends into characters. I'm tired of decoding stuff only for it to be something banal.
I'm in two minds whether to carry on. What I thought was a charming game has turned into something that I spend a lot of time looking at with a furrowed brow. I don't think that's a good thing.
I'm really surprised you haven't found the lever to drop the water level yet; it's not that far off from the bell tower. In any case, that door requires all 64 cubes, so you won't be there for awhile, if at all. I don't think anything else is revealed by the drop in water level; maybe a door somewhere.
The stone thrones (you should read this so you don't get aggravated at it; it won't ruin anything for you):
Go find the blue columns with a hollow section at the top and look around on the ground, for starters. You should also find all tetromino sequences easier to read, as well as the coded alphabet. As for it being banal, almost all of the writing on the walls is just flavour text, and nothing any of the characters who speak the code have to say is important.
I've started up the new game + after wondering how the game had possibly already finished with so many mysteries in the air. Turns out these new glasses are about to come in handy, I'm just starting over again but already I'm looking about the boiler room on the first stage and piecing together the tetris piece conversions which will hopefully bear some fruit especially at the button prompt cube that left me bewildered earlier. I'm intrigued of the skull artifact as it's the only one missing but with the collections starting to come together I'm in a good position to start moving on.
So, in short... without looking at too many of the other spoiler tags in the thread, this effort probably hasn't even started yet
Working together to solve the cipher. And, I guess, sharing secrets of the slightly harder anti-cubes.
At least, that's all I ever understood to be it. Didn't really get that, though, since I worked it all out on my own. The only thing that was genuinely a community effort was:
A room somewhere (near the bell tower, I think) that contains a giant, black prismatic slab (it might have required a code on a treasure map to appear or something). Referred to as "The Monolith", there is absolutely no hint given to solve it. There is a space that you must stand in and enter a specific code that there is no way to find.
The only way that it was solved was with brute force: A few people set up a site that would randomly generate a sheet of codes, such that everyone who visited it would get a different set of codes to attempt, running through every possible combination of button presses and stick movements. Eventually, someone found the code; and even then, no one has been able to reverse-engineer it to find any sort of clue in the game that would lead to it.
Some reckon that it was designed to be crackable only with brute force.