Re. WotC's site -- I thought the same when I saw what direction the judges were heading in. But every one of them agreed on this nomination, and their reasoning convinced me pretty quickly (not that I had any choice in the matter!).
WotC's website may have it's problems, but the sheer amount of D&D resources, freebies, enhancements etc. definitely qualifies it for a nomination along with the others. Now it's the fans decisions as to whether the navigation/availability are more/less important than the content.