My answer would be a bit different if I wasn't constrained by the parameters of the movie, but the way I took it was that any system setup without the power of true choice would fail. Create a utopia (garden of eden) - fail. Create a world with just basic cause and effect - fail. But create a world where everyone has an impact, and the human mind accepts it, implying if anything, that we are innately used to free will. Even the architect (the creator of the system as a whole), is bound to offer choices. Maybe the real message would be the one that those who can go beyond the choices available (survive when you're supposed to die, break the boundaries of time and space, etc) you can be the ONE. That's all fine and well for the movie, and although many of us can fly with our eyes closed, for the time being I'm not saying your life purpose should be to fly.
All that being said, I don't think people are stupid as a whole. If I had to choose on attribute, it would most likely be between the crossroads of fear and yearning.