"if Harry is so smart, why hasn't he figured out the solution to the problem that most of the audience has figured out by now?"

Please remember that the audience has a lot more information on the subject than Harry himself, for not only do we get to see whats happening in the scenes of the story without Harry in them, we also have the huge advantage of having read the canon Harry Potter books. As Quirrell worked for Voldemort in canon, our prior probability that Quirrell is working for Voldemort is high, even before we read HPMOR. Harry on the other hand, hasn't even had a reason to consider that this is a possibility, let alone to assign a high probability to it.