I try to keep up with Khoi Vihn and Subtraction because I believe he always provides a balanced insight into respectable/high-design principals and the practicality of applying them to mammoth operations like the NYT and such.
In fact, his tone of decency and respect, despite the the off-the-cuff pronouncements made by Andy Rutledge is exactly the voice I've come to expect from Khoi. Which is awesome.
Also, this reminds me a lot of the Delta Airlines redesign fiasco brought on by another designer (http://www.dustincurtis.com/dear_american_airlines.html). It's really easy to sit back and critique the obvious flaws in design from within the ivory tower of photoshop, where you can arbitrarily remove advertisements and ignore the loads of user studies that entire teams have spent significant portions of their careers.
This is the kind of stuff that gives designers the MO of being 'decorators' who don't 'respect constraints' - operational or technical. As a designer myself, it's sad to see this behavior showing up again and again.
The only really egregious criticism was that "the front page of a news paper is not editorialized". Someone DOES choose what the most important stories are at the time of publication and puts those on the front page. That is editorializing. If all the stories were in reverse chronological order or alphabetical order or something, then it wouldn't be editorialized.
All the "terrible/unusable design" criticisms are quite valid today, I think. Maybe they weren't 5 years ago when the site was designed, but there is simply too much information to process now.
"The New York Times presents a rather typical example of terribly-designed news"
"popularity has nothing to do with news"
"today's paper: irrelevant"
"the Times’ search results page is an excellent example of usable news design"