I like the clean typography, and appreciate that they were content with subtle changes rather than something "radical." But why, oh why, did they add one of those horrible floating bars at the top of the screen? Those things almost always break page-down, yo!
The only time I dislike the top bar is when they're too tall or there's not enough height in the view port. I think this one is as good as they get, though. I do wish they only enabled it at a minimum height. Designers only seem to think about min-width, not so much min-height.
True, I can still hit the space bar, but it does something different and broken. Try paging down on HN, and you'll see that the bottom 1-2 lines are preserved at the top of the screen, so you don't lose your place. Now try it on NYT: at least for me, there is absolutely no context preserved. That's better than the all-too-frequent case where a line is missed entirely, but it still makes reading harder. Plus, I'm so used to lousy sites that skip a line on page-down that I don't trust the NYT's version not to do so.
EDIT: They seem to do the right thing on articles, but not on the front page.
The front page is working correctly for me in Firefox 26. When I hit page down or space the two lines that were at the very bottom of the screen move to just below the top bar.