The choice of words is curious to me, because while i believe it was "close," i disagree on the "controversy." For every person who says that Pacquiao "clearly" won, there's probably and equal number who would say he "clearly" lost. In both cases, it's really only as clear as mud, which is why we needed the judges to render a verdict.
I personally agreed with the judges on this one (my opinion on the scoring was near-identical with the "Lederman Scorecard"), and i think that while Pacquiao's inability to beat the feisty Marquez to a pulp was a disappointment, it is not enough reason to award the win to the latter. The fight went down the wire, and in the end the judges did what they were supposed to do: they judged based on how they thought it should be judged. On this particular night, they thought that more punches taken/landed made the better fighter, so Pacquiao won. If they had felt that better defense and more counter-punching would have been a better benchmark, then Marquez would have won.
It's a little weird to me to take the booing crowd into consideration. More people sang the Mexican National Anthem than the Lupang Hinirang; doesn't that in itself indicate that the audience consisted of either more (or more vocal) Mexicans than Filipinos? Lovers gonna love and haters gonna hate. Personally, i'm looking forward to the fourth installment on this one.