The puzzles are the secrets of Isola. Or something like clues leading up to revealing the cave. Once the boulder is removed the villagers can go inside and see that someone had been in there. I believe in V.V.2, the villagers will find a way to another part of the island from inside the cave. It's just that the game did not have quite the climatic ending we had all hoped for. Until then, when you solve all 16 puzzles, you've discovered the "secrets" of Isola.