I don't think that "how not to design a website" is quite fair-- they just haven't overhauled the design for over five years, and design trends have completely changed in the meantime. At the time, the current design was innovative (with Khoi Vinh bringing the typographical grid to web prominence with it) and consequentially cleaner than every other news website. The clutter also skeuomorphically evokes the idea of a newspaper (though this isn't necessarily desirable and probably what you mean by "start from scratch.")
Although I'm excited for this new design, I think it's important to recognize the merits of the old one.