Late to the party but now as the theme went live on my favorite site (Ask Ubuntu) there are issues beyond of what I feared.
Often I have to work on small screens (office computer, netbook) where not much space for content is left if we deduce all windows decorations, top bars, bottom bars, side bars, and whatnot from the visible are:
This was already an issue with the old design but it sadly could not be improved with the new theme. The left side menu is a great thing. I like it a lot but it needs to hold many more items than now. Much of the top bar items could reside there.
So here are my suggestions for great improvements that could be achieved with only very little changes to the overall site design:
Move the broad top bar with the site logo to the side menu to keep it sticky so that we still know on which site we are when scrolling down through questions.
Leave Beta on the non-sticky colored top bar which would move away on scrolling to have the site logo small enough to fit the side menu.
Newest, Featured, Frequent... go to a submenu on the "Questions" side menu entry. Even a dropdown could be considered there.
The Ask Question button moves to the side menu where it would be sticky too. A good place appears to be e.g. directly under the site logo. By this the Ask button is accessible from everywhere.
The question count goes to the title where All needs to be replaced by the display options we chose (e.g. Active, Newest, Unanswered)
To illustrate all this better here are screenshots from only few changes needed to the source:
Landing Page for Active Questions display
Same page scrolled down
An additional minor improvement was moving the search field a bit to the right to better align with the left side menu.