I had to try, but I think in the end I agree with percusse: It's a littletedious. You can use two axis and use the (so far quite convineant) bar shift=<lenth> option, however, depending on the width of the picture, you'll have to experiment a little. Furthermore, you have to use the ymin=<number> and ymax=<number> as otherwise the y-axes won't align properly. Here's an example to illustrate it cane be done with a little hassle:
Code
\documentclass[parskip]{scrartcl}
\usepackage[margin=15mm]{geometry}
\usepackage{pgfplots}
\pgfplotsset{width=10cm}
\begin{document}
\begin{tikzpicture}
\begin{axis}[ybar stacked,bar shift=7pt,ymin=0,ymax=11,symbolic x coords={A,B,C,D,E}]]
\addplot coordinates
{(A,1) (B,1) (C,3) (D,2) (E,1.5)};
\addplot coordinates
{(A,1) (B,1) (C,3) (D,2) (E,1.5)};
\addplot coordinates
{(A,1) (B,1) (C,3) (D,2) (E,1.5)};
\end{axis}
\begin{axis}[ybar stacked,bar shift=-7pt,ymin=0,ymax=11,symbolic x coords={A,B,C,D,E}]
\addplot+[fill=blue!50!gray] coordinates
{(A,1.5) (B,1.5) (C,3.5) (D,2.5) (E,1)};
\addplot+[fill=red!50!gray] coordinates
{(A,1.5) (B,1.5) (C,3.5) (D,2.5) (E,1)};
\addplot+[fill=yellow!50!gray] coordinates
{(A,1.5) (B,1.5) (C,3.5) (D,2.5) (E,1)};
\end{axis}
\end{tikzpicture}
\end{document}
Result

ybaror theybar stacked. It seems like feature request for a possible mixture of the styles. You can try to place an empty axis on top and shift the bars of the second axis but still it would be a tedious hack. – percusse Sep 08 '12 at 23:45