I ran into an issue recently where an author wanted some soft emphasis in her essay changed to hard emphasis with em dashes. This was throughout most of the essay, and I had to copy and paste em dashes from Microsoft Word.
In the version of this essay -- http://www.electronicbookreview.com/thread/firstperson/generational -- on the new interface, Ben Underwood's gloss is missing; instead there are two versions of the Harrell gloss. This is especially problematic because the Harrell gloss refers to the Underwood gloss. I wonder if this speaks to some deeper problem? NOTE: BOTH GLOSSES ARE MISSING NOW.
In the past, secondary-threads had their icon display slightly apart from the the main icon. I might be missing it, but it looks like there is no visual representation of secondary threads on the new website. If that is the case, I think it would be nice to get something equivalent to the old website display on the new website.
On the main page, some of the icons blend together. I like the new, simple look of the icons, but I was thinking that a thin (1px) black border around each might help to visually distinguish them from one another.