I....... have to disagree, though I'm not sure why, but that old one looks much better to me. Like it's simpler and more clear.
The sidebar it had seems to waste too much space, though. It's just 5 links meant for navigation. They'd be better arranged horizontally. I can agree that it's clearer than what we had a few days ago, having only 1 navbar instead of 2, but that's also because it has a lot less features than GitHub has now.
The 2013 version by comparison wastes horizontal space while surfacing less information. The contrast is worse and there isn't enough to visually distinguish the four (!) rows of headers. Personally, I also find the navigation box on the right to be weirdly sunken into the page and I think the color scheme has been greatly improved.