No matter what your criticisms are of the finer points of his critique (I agree with some, not others), the OP mocked-up a much better concept for the site. (IMHO)
In the Stack Overflow podcasts, that is the one app they strived to be so vastly different from.
Nice try, but he needs to have a clue of what he's trying to design.
However, Stack Overflow is a business and I think moving the ad banner like that would have some big implications in terms of conversions. Also, the tagging system, which is a key navigational element as well as potential revenue source (sponsored tags) is removed.
Also, another thing I disagree with is the change in proximity of the user image to the voting icon. I think psychologically this has some implications because it now looks like you are upvoting the user vs. the information presented.