I've been searching this for hours, but didn't find a reason for this behaviour:
Here is my example:
\documentclass{article}
\usepackage{tikz}
\usetikzlibrary{3d}
\begin{document}
\begin{tikzpicture}[x={(0.866cm,0.5cm)},y={(-0.866cm,0.5cm)},z={(0cm,1cm)}]
\fill[blue!50,opacity=0.6] (0,0,0) rectangle (2,1,0);
\fill[green!50,opacity=0.6] (0,0,0) -- (2,0,0) -- (2,1,0) -- (0,1,0) -- (0,0,0);
\draw[->] (0,0,0) -- (1,0,0);
\draw[->] (0,0,0) -- (0,1,0);
\draw[->] (0,0,0) -- (0,0,1);
\begin{scope}[xshift=3cm]
\fill[blue!50,opacity=0.6] (0,0,0) circle (1);
\draw[->] (0,0,0) -- (1,0,0);
\draw[->] (0,0,0) -- (0,1,0);
\draw[->] (0,0,0) -- (0,0,1);
\end{scope}
\end{tikzpicture}
\end{document}

I'd expect both rectangles to be painted the same. To be more precise, both should appear like the green one, but the don't.
Obviously, the coordinate of the upper right corner (2,1,0) is correct for both rectangles, but only the green one correctly aligns with the coordinate system's axes.
In comparison to this, the circle correcly uses the modified vectors, since it is drawn as an ellipse.
What do I have to do, to get the blue rectangle painted like the green one?
Edit: I found something interesting in this answer. Apparently the following code works, but I find it a little inconvenient to place all my rectangle into scopes.
Additionally, is canvas is xy plane at z really implemented the wrong way? Why isn't this fixed, then?
\documentclass{article}
\usepackage{tikz}
\usetikzlibrary{3d}
\makeatletter
\tikzoption{canvas is xy plane at z}[]{%
\def\tikz@plane@origin{\pgfpointxyz{0}{0}{#1}}%
\def\tikz@plane@x{\pgfpointxyz{1}{0}{#1}}%
\def\tikz@plane@y{\pgfpointxyz{0}{1}{#1}}%
\tikz@canvas@is@plane
}
\makeatother
\begin{document}
\begin{tikzpicture}[x={(0.866cm,0.5cm)},y={(-0.866cm,0.5cm)},z={(0cm,1cm)}]
\begin{scope}[canvas is xy plane at z=0,transform shape]
\fill[blue!50,opacity=0.6] (0,0,0) rectangle (2,1,0);
\end{scope}
\fill[green!50,opacity=0.6] (0,0,0) -- (2,0,0) -- (2,1,0) -- (0,1,0) -- (0,0,0);
\draw[->] (0,0,0) -- (1,0,0);
\draw[->] (0,0,0) -- (0,1,0);
\draw[->] (0,0,0) -- (0,0,1);
\begin{scope}[xshift=3cm]
\fill[blue!50,opacity=0.6] (0,0,0) circle (1);
\draw[->] (0,0,0) -- (1,0,0);
\draw[->] (0,0,0) -- (0,1,0);
\draw[->] (0,0,0) -- (0,0,1);
\end{scope}
\end{tikzpicture}
\end{document}



canvas is xy plane at zis really implemented the wrong way: Judging by the fact that it doesn't work in its current implementation, but it does with the correction, I would say "yes". It probably hasn't been fixed because no bug report has been posted. – Jake Apr 11 '13 at 14:49canvas is xy plane at zapproach works for you in principle: You can define a convenience style using\tikzset{3d/.style={canvas is xy plane at z=0}}. Then you can draw your rectangle using\fill [3d] (0,0) rectangle (2,1);, without the need for a scope. – Jake Apr 11 '13 at 15:04