Dear god, where to start. I worked on the Times web site for 7 years (dev, not design). Before I even saw his "redesign" I read his preamble. First, lets be clear, he is working from the wrong assumptions. He demonstrates clearly what is wrong with many news outlets but then he lumps the Times in with them too. Since his piece is about the Times I have to feel all assertions he makes are about that too, and not just media in general.

  Digital news is broken. Actually, news itself is broken. 

No its not. The business model is broken. Print is declining. Online revenue is being experimented with. Could be better, could be much worse.

  Almost all news organizations have abandoned reporting in
  favor of editorial; have cultivated reader opinion in
  place of responsibility; and have traded ethical standards
  for misdirection and whatever consensus defines 
  as forgivable. 
 

Please don't lump the Times in this category. They have a small amount of clearly stated Editorial content. Separate from that is the Opinion pages, and what is completely separate from that is News (thats the bit where they try their damnedest to keep Opinion out of it and cite sources, provide analysis and present facts).

  And this is before you even lay eyes on what passes for
  news design on a monitor or device screen these days.

We'll get to this part...

  In digital media—websites in particular—news outlets 
  seldom if ever treat content with any sort of dignity
  and most news sites are wedded to a broken profit model
  that compels them to present a nearly unusable mishmash
  of pink noise…which they call content.

Actually that "broken profit model" isn't broken for some but thats another argument. If you have ever sat in a newsroom meeting, or a design review, or a meeting where product people spar with editorial who spar with developers you would realize that dignity is a big deal. A big FUCKING deal. You might not like the fruits of that but don't never say they don't give a shit. The Times prizes content to a fault.

  In an effort to disguise and mitigate the fact that they
  have little idea how to publish digital content 
  properly—often sneakily called "differentiation"—some
  news outlets release apps for digital devices. These 
  apps typically (but not always) do a better job of 
  presenting content and facilitating navigation, but
  they’re a band aid on a festering abdominal wound. 
  Digital media is simply digital media; if you do it 
  right you publish once and it works anywhere. If you’re
  using an app to deliver content, you’re doing it wrong.

First, its not clear that this criticism is Times specific. However its still wrong. I've been in plenty of meetings with bright people from inside and outside the company where we started off with the goal that, as he put it, "if you do it right you publish once and it works anywhere". It didn't work. These were not just "old media" types either - these are talented people, some of whom who don't even read the print edition. gasp

Its something thats very easy to say - hell I wish it were true. It is not. Devices, apps, platforms, whatever. They have strengths and weaknesses. You can not have one magic solution for all. This is a crappy comparison but its a bit like saying you have one single car for every type of terrain - same car for soccer-mom and deer-hunter alike! Sweet!

  Instead of working with a handful of redundant, 
  mitigating formats (websites, mobile sites, apps, etc...)
  for content delivery to popular devices, news 
  organizations should simply deliver it correctly in
  the first place, one time; using html, css, JavaScript,
  ...oh, and design. The employment of content design
  would be quite refreshing, actually.

Sadly, this is very much an example of a person looking in. I'm not sure how to counter this. Its simply a matter of not knowing what happens on the 7th floor of the Times Building. Nor could he. However I can only assure you that a very dedicated group of Designers are actively working on NYTimes.com and they know their shit.

There is definitely a crap load of work to do to fully redesign a web site that was last done in 2005 - but it does happen. A couple of URLs come to mind which are not illustrated in his piece:

Opinion (redesigned last year)

http://www.nytimes.com/opinion/

http://www.nytimes.com/roomfordebate/2011/07/25/how-budget-c...

http://www.nytimes.com/2011/07/26/opinion/26brooks.html

Times Skimmer

http://www.nytimes.com/skimmer/#/Top+News

Books / Best Sellers List

http://www.nytimes.com/best-sellers-books/combined-print-and...

T Magazine (CHECK THIS ONE OUT - you seem to have missed it Andy!)

http://www.nytimes.com/pages/t-magazine/index.html

http://www.nytimes.com/gst/tmagazine/video/index.html

Dealbook Blog

http://dealbook.nytimes.com/

Business Day Sectionfront

http://www.nytimes.com/pages/business/index.html

LENS Blog

http://lens.blogs.nytimes.com/

Times Machine

http://timesmachine.nytimes.com/browser

Opinionator Blog (my favorite design)

http://opinionator.blogs.nytimes.com/

Slide Show (Great Homes)

http://www.nytimes.com/interactive/2011/07/20/greathomesandd...

So whats next... well too much actually. I do not have the time nor the patience to dig at all of Andys points. Im sure not all of them are bad, but there is enough there to make me wonder whats wrong with this guy. Again, he is a professional. I am sure he has had critics of his work, and he knows that there was an inner process where a lot of those points were brought up and shown not to hold water. He is now doing the same thing.

So I'll leave it on one final point. Mobile Sites. Its an example of what happens when you don't know that the Times is aware of his point and we discussed it and there was a damn good reason we made the decision that we made.

What am I talking about? He shows the iPhone with the full NYT homepage and has the caption "Um, are you frisking kidding me?". In other words why not a mobile site.

Well, very simple. The iPhone is capable of rendering and interacting with the full page. It was the first browser to do so - it don't require a lite version. You could tap, zoom, pinch, drag and get the full depth of the page. Other browsers - like those for Nokia, RIM etc couldn't handle that.

This was talked over to death. There were compelling arguments about going down this road - or not. In the end, the decision was made to NOT redirect those advanced browsers to the mobile site. You can still go to m.nyt.com if you like, we just wont force you too.

  but it should not require anything more than a media 
  query fetching different CSS and perhaps some additional
  scripting so as to simply restyle the content experience

Andy does say that all you need is media quires for the CSS and such and bingo. Well, no. No its not that simple. If you want to redo the homepage for a specific mobile experience then you probably want to serve different sized images, maybe not have some Flash stuff on the iPhone, maybe drop the bandwidth intensive stuff that works well on desktop.

CSS media queries does not solve the problem. It is never that easy and shame on your for saying so. You are a professional. You should know better. Bad Andy. Bad. No biscuit for you.

Man, this makes me bitter. RANT OFF.