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My personal opinion...
Probably the most notable change has been done to the code blocks by adding syntax highlighting (Using a variation of the Midnight Theme from Syntax Highlighter ). The download link has been removed as users can simply double click on the code block, revealing the selected plain text.
That's not working too well, since even the "plain text" still has its lines wrapped with the + in front of continuation lines. So it's not a good substitute for the download link.
Personally, I hate this. I'd rather have three times as much space taken up by something that doesn't stay on the screen all the time as opposed to the permanent stuff.
Organized the poster's name, date, number of replies and link to post reply into one visual unit above the post title. I wanted something to create a tightly grouped navigation bar for each post that will always be in the same location. (An example would be in regards to 'Offer your reply' which can shift depending on the length of a particular post.)
The separation looks wrong to me. When I glance at the page I immediately think of a post as what's between two gray bars. While in reality the it's what's between the two barely visible dotted lines. Personally I'd move the author etc. line below the gray bar and just remove the dotted line altogether.
There's something similar on the righthand column. The change of background color for the chatterbox input line makes it appear as if it's actually a new section, especially since the change in background color between login section and chatterbox does the same.
The increase in size of the righthand column isn't my cup of tea either. I'd prefer to keep the main column as wide as possible. From the looks of it the main reason might be an increase in font size?
In general, all the background colors seem to give the site somewhat of a claustrophobic look compared to the current one. Perhaps changing the background of the main section back to white and lightening up the rest might help some with that.
On a nitpick note, what's with the question mark after each header in the right column?
I'm afraid I'm far better at expressing things I don't like than things I like, but I hope at least some of these comments might be useful.