The design has its moments but I actually like NYT. The only thing I would like more is fixed dimensions for items on the front page, maybe 2 column layout with both sides perfectly aligned per item. The draw of newspaper sites is both the quality content within articles but the curation of articles themselves so having everything in uniform lists is too confusing. Additions I wouldn't mind are most tweeted or tweeted by your friends type social media integration.

If design was the only thing killing the newspaper industry their problems would be solved.