EDIT: I don't really read Kotaku, but I read Lifehacker and they have the same layout.
That's because they are sister blog sites under Gawker Media... ignoring my opinion of Gawker Media in general (which to put it kindly isn't that high), they actually announced this change was coming up with a preview a while back, so it shouldn't have come as a big surprise (I don't even follow any Gawker blog that much, and still caught it since it was cross-posted on a blog aggregator)
Edit: looking at the design, there are really only two things I consider negatives:
1. The panel is on the right side, I don't like right-side panels when everything is center-aligned
2. Because everything is center-aligned, there is a LOT of whitespace, which is just a waste.
Basically the actual story should take up all the space of it currently + the panel and the panel should be flush to the edge of the browser on either side. I've never been a fan of sites that squeeze panels next to the text, even moreso for right-side panels.
Then again I'm not really a big follower of Gawker Media, so I guess the "old" way never grew on me