First: I like the new design! It is great.
One minor detail is the FavIcon color and its transparency. In my list of tabs and bookmarks it is dull and doesn't stand out. (I'm using Chrome here)
In my Favorites tools bar: You can hardly see the S and the hexgon-lines are almost invisible, only some colored dots remain.
As active and inactive tab:
Even as Twitter icon it is 'white', 'blank':
Compare it with other SE icons:
More general
It's probably the overall look-and-feel of the logo, great idea, but lacking 'power' (like the tipping beeker, the StackOverflow logo, the English logo, the Gaming logo) See this list, almost all logos have strong colors and stand out as icon.
