Though there are a number of plot points left hanging (presumably to be answered in the, I hope, soon to be made sequel), I thought most of the clues were left in plain sight. What I found interesting, in my travels through my social networks, was the hatred that many of my fellow nerds had for the movie. Then I saw the pattern. Most of the people who really disliked it were hardcore, fundamentalist atheists.
I'm sure there are other people who disliked it, for various reasons. But amongst my friends, the ones who had the most problems with it were atheists, usually of the Dawkins-boosting variety.
I have to admit, I found the "I choose to believe" stuff a bit eye-rolling myself. Nothing gives people of faith a bad name more than the artistic portrayal of intellectually slothful, baseless believers who have no rigor to their worldview. They bug the crap out of me, frankly. Any faith that stands or falls on feelings seems to me to be worth very little. On that level, unfortunately, the movie fails. It would have been so simple to have one of the scientists say, "We're proceeding on a hypothesis. We're checking this hypothesis against the available facts. Once we have some kind of sense of what these facts are, we'll modify our hypothesis and try again." This is stuff that you learn in Middle School.
I still thought it was awesome, though, as a terrible-shit-is-about-to-go-down thriller. I just notice when my atheist friends get bent out of shape, and I can almost always predict when it's going to happen and why. Whenever anybody says they believe for no good reason, it just gets up their noses. It gets up my nose, too, but for totally different reasons.