The New York Times built the current site in 2006. The Times just announced that they have are working on a new site design (and presumably completely new architecture) for the last year and should release it soon.
There is a world of difference between doing a cute vanity project that works for say 99% of the time but doesn't mean that they buckle down and do the hard work involved delivering a major publishers site.
Another example Google has a lot of smart people but they cant parse a robots.txt file with a BOM in it.
There's a ton of product manager, designers, and researchers on Hacker News. But looking at his profile seems to indicate that Mr. Clarks a pretty humble guy.
Which means... unique user page views with 0 engagement metrics! Yay~
MAU and DAU are meaningless statistics. It's pure eye-views, that's all.
Show me some average aggregate visits per user per month, and I'll believe there's actually something happening (ie. the average number of times each unique user visited the site in a single month. Hint: for Facebook, this number is probably ~20-30).
Are you sure? It's better, yes, but it's not a model of UX and on an iPad it seems not much thought was taken into making it a truly universal app. There's a lot of unused space and everything is too large.
The Google+ app with its combo of Path and Flipboard is a much better model to follow. Fast, and it takes advantage of the screen size in both versions.
See http://open.blogs.nytimes.com/ and http://www.nytimes.com/projects/2012/snow-fall/
So they have the skills, but maybe it's for other reasons they don't follow those practices.