Here's the thing: When was the last time you gave a damn about the section?
I understand caring about Fashion vs the Science Times. But while the number of sections the Times has makes sense in print, on the web, the differences between the Metropolitan, New York, Business Day, International, National... it all seems fairly artificial. Is the war in Afghanistan national, or international news? Does education reform go under politics or education? The answer is, of course, both, but the Times has to choose. Sure, it makes sense to group them on paper, because it's the best way to help you find things that are like what you're reading. But digitally, without the ability to quickly flip through, there's a lot that just gets hidden from the reader.
As someone who spent five hours yesterday laying out a newspaper, I have a lot of respect for the designers at the Times. Here's to hoping they find a better way to move their IA to the web than in hundred-year-old silos.