(Spoilers) Late-Game Help?

Without giving too much away, can someone tell me if I'm supposed to reach a point where it's no longer obvious what to do? Or have I just missed something simple?

Just to give you an idea of where I am:

• I've activated (all?) ten lasers.
• I've found one solution to the puzzle at the top of the mountain with the two men standing on it. The other two solutions seem impossible with the men there.
• I don't remember any other puzzles that I left unsolved. (Though I'm not certain there aren't any.)
• I solved the RGB puzzle in the town, but I couldn't tell what it did.
• I've found at least five doors that I can't get through because I'm on the wrong side of them.
  1. In the tunnel right below the sun temple's laser.
  2. In the tunnel below the windmill.
  3. In the town.
  4. In the cavern behind the huge woman, hidden by plants.
  5. On the hillside near the woman with the palette.
• I've found four of the six hexagonal paths (#1, #2, #3, and #6) and watched their videos in the theater. I don't know where the other two chambers could be.
• I've found a lot of the shapes on the black obelisks, but not all of them.
• I've been running around the island looking for new things to interact with, but I haven't found anything recently.
• I know that the pond is a map and that the lanterns are lasers. I'm pretty sure the fountains are obelisks, and I think the clams are secrets, but that hasn't helped me.

Thanks!