Let's be honest about what this all really about. The new 538 website has been a colossal failure. It's been widely panned for having superficial and obvious political analysis, relying heavily on cultural fluff pieces that no one wanted or cares about (best burrito in America??), and embarrassingly poor predictions (7-1). Since July, its traffic has been slowly but steadily falling. The site's forecasting model is no longer new or fresh; seemingly every big news site has one now, and they were all released before 538's, spoiling whatever big bump 538 hoped to gain from releasing their model. So Nate Silver is drumming up some controversy in a transparent and desperate attempt to get some publicity and page views.
I totally agree that the new 538 is pretty disappointing, but this doesn't change the fact that Silver is right on the statistical issues.