I think the issue with the BCS is that there is too much human input - yes, too much human input. People get too emotionally involved, and like was said, late losses hurt worse than early losses when people do the rankings. The computers take the entire season into account, and compare teams statistically and based on strength of schedule better than I think the AP, coaches' or any other human pole could. I don't think that the human polls should be removed from the BCS formula, but that they shouldn't have as much weight.
While we're at it, I think the human component should have a better, more objective and unbiased viewpoint than either the AP or the coaches. I've never liked the AP poll, and you can't tell me that anyone who votes in the coaches' poll actually sits down to watch enough football to really rank the teams. There must be a firm somewhere capable of reviewing and breaking down every single game in each of the BCS conferences to add a qualitative input to the polls.