Well, that's not entirely true either. There is some over-arching mystery to the Stone that you are supposed to solve, complete with various enigmatic references implying the owls are not what they seem, and so forth. Solving the lesser puzzles is supposed to help you solve the Enigma or the main puzzle. They're pretty fun on their own, though - which is good, because in spite of the hushed tones and hints of further Things To Be Revealed, I couldn't begin to guess where things are supposed to be heading.
A couple of years ago, I ran into a wall and got really stuck on all of the puzzles available to me (the more you solve, the more you get access to), and I sort of lost interest. I had some bandwidth issues, too - trouble getting into the site at least, for some combination of reasons.
I got an email today, though, talking about some game-related gatherings this year. So I logged back into the site, and with the help of Google promptly solved the puzzle I'd particularly been banging my head into the wall over. (Yes, I know much of my game activity took place pre-Google, or at least before I knew anything about Google - it's amazing how much nicer research can be with a decent search engine.)
So I guess I'm back into the Stone again, for a while. It will be interesting to see if they've become any more forthcoming about the mystery behind the mysteries, so to speak.