I'm gonna be that guy - I prefer the appearance of the blue version. Things stand out more, it's seems easier to parse. The grey looks all washed out and nothing really sticks outs. The layout of the right-hand panel is an improvement though, definitely.
I went back and forth between both for a couple months and I can assure you that the new design is much better. It looks overly subtle now, but after your eyes and brain get used to it, you'll think the blue one was hideous.
I agree that the new styling a lot better with regards to positioning and sizing etc. but the colour scheme doesn't have enough contrast IMO. But I'll give it some time to get used to :)
There's less contrast now, and people with any vision trouble will have additional problems. In the before and after of the reading section, the items in the right-hand column aren't even visible at all. It's white on s super-light cream color. Author & designer both need to look at http://contrastrebellion.com/