As mentioned elsewhere, you seem to think that people don't actually use their screen real-estate. You are throwing away nearly a quarter of my browser's horizontal space for empty regions which fail to contain my gaze in the information I care about. You then go and give two-fifths of the used space to the right-hand side-bar which contains your adverts, yes, but it also means that the region remaining for the story summaries is inadequate. If I have the images on, many summaries require scrolling to get through.
The stalking header bar is useless. It contains links to things which I might want to utilize upon visiting, but when I am paging down to read stories, I'm not suddenly going to think, "I need to submit a new link." or "I can't remember what site I am on and need a link to it.". It just steals vertical space in a world where people have an excess of horizontal space on their screens. Stalking elements also break the idea of a web page of being a page which the user is examining through, which is not only creepy, but it makes it more difficult to maintain a spatial awareness on the page.
There is insufficient visual hinting regarding the boundaries of stories. Visual hinting allows people to more efficiently navigate information by ignoring what isn't important to them. In particular, the story titles are in a font which takes up too much space (too many stories have multi-line titles) and the font weight is so low as to not give them sufficient contrast. Speaking of contrast, the light grey frame is far too weak to create a box for the story. You also are trying to use white space to organize the data within a story element, but it just means that nothing in it anchors the reader's gaze requiring constant reevaluation.
Comments are just fucked. You have thrown out a somewhat successful threading system for an unnavigable mess. Even more than stories, the ability to skip comments is essential to find the parts of a conversation the reader finds interesting. The lack of width and size of overhead for each comment, plus the fact that auto-minimizing of comments isn't functional makes it just a stream of awful.
For all of the slamming of skeuomorphism and seeming praise for iconocentric user interfaces which gets promoted on this site, this pedestrian redesign to look like an AOL blog site is utter crap. Are there improvements to be made to the old design? Absolutely. It would be less offensive if this particular redesign was actually trying something new instead of regurgitating the crap which is already out there.