You can obtain the effect you want as follows:
\documentclass{beamer}
\usepackage{tikz}
\usepackage[absolute,overlay]{textpos}
\textblockorigin{0mm}{0mm}
\begin{document}
\begin{frame}[t]
\pgfdeclareimage[interpolate=true,height=\textheight]{layer1}{circle}
\pgfdeclareimage[height=\textheight]{layer2}{square}
\begin{textblock}{1}(0,0)
\begin{tikzpicture}
\only<1>{\node[opacity=1]{\pgfuseimage{layer1}}};
\only<2->{\node[opacity=0.5]{\pgfuseimage{layer1}}};
\end{tikzpicture}
\end{textblock}
\begin{textblock}{1}(0,0)
\begin{tikzpicture}
\only<2>{\node[opacity=1]{\pgfuseimage{layer2}}};
\only<3->{\node[opacity=0.5]{\pgfuseimage{layer2}}};
\end{tikzpicture}
\end{textblock}
\end{frame}
\end{document}
This displays a circle in the first slide, and in the second a square in full opacity circumscribed in the circle which is 50% transparent.
All the magic is in the definitions at the top of the file. The only unique things in my slide content itself is that: 1) I did not leave a blank line before and after \[...\] equation construct; and 2) the \columnskip specification mentioned below.
Here I addressed normal text, equations, centering, center environment, itemize environment. EDITED to address columns environment. I have REEDITED to introduce the macros \stretchon and \stretchoff to make this process selectable. Just issue one of these commands between frames to change the current mode. I have also REEDITED to provide the redefined \item with an optional argument, as it should be.
Generally, the main thing is to redefine \par to add a \vfill after the \par. However, a few additional refinements are required. The first invocation of \item in an environment should just use the regularly defined \item, but then redefine \item to add a \vfill prior to subsequent \items. Environments like center and itemize also may need to reinvoke the \vfilled version of \par, either coming into the environment, leaving it, or both.
In my edit to address the columns environment, I determined that \vfill solutions seemed to have no effect, which must have something to do with the way the two columns are separately constructed and aligned. So my solution was to introduce a length \columnskip, which will be the \parskip introduced between items in the column environment and upon exiting that environment. Thus, for any particular slide, one may have to adjust it once or twice to get a good match to the remaining \vfills on the page
\documentclass{beamer}
\def\itemsymbol{$\blacktriangleright$}
\let\svpar\par
\let\svitemize\itemize
\let\svenditemize\enditemize
\let\svitem\item
\let\svcenter\center
\let\svendcenter\endcenter
\let\svcolumn\column
\let\svendcolumn\endcolumn
\def\newitem{\renewcommand\item[1][\itemsymbol]{\vfill\svitem[##1]}}%
\def\newpar{\def\par{\svpar\vfill}}%
\newcommand\stretchon{%
\newpar%
\renewcommand\item[1][\itemsymbol]{\svitem[##1]\newitem}%
\renewenvironment{itemize}%
{\svitemize}{\svenditemize\newpar\par}%
\renewenvironment{center}%
{\svcenter\newpar}{\svendcenter\newpar}%
\renewenvironment{column}[2]%
{\svcolumn{##1}\setlength{\parskip}{\columnskip}##2}%
{\svendcolumn\vspace{\columnskip}}%
}
\newcommand\stretchoff{%
\let\par\svpar%
\let\item\svitem%
\let\itemize\svitemize%
\let\enditemize\svenditemize%
\let\center\svcenter%
\let\endcenter\svendcenter%
\let\column\svcolumn%
\let\endcolumn\svendcolumn%
}
\newlength\columnskip
\columnskip 0pt
\begin{document}
\stretchon
\begin{frame}{A few paragraphs (with stretching)}
As any dedicated reader can clearly see, the Ideal of practical reason is a representation of the things in themselves.
I have shown elsewhere, the phenomena should only be used as a canon for our understanding.
The paralogisms of practical reason are what first give rise to the architectonic of practical reason.
\end{frame}
\begin{frame}{Displayed Equation (with stretching)}
As any dedicated reader can clearly see, the ideal of practical
reason is a representation of the things in themselves
I have shown elsewhere, the phenomena should only be used as a canon for our understanding.
\[
x^2 +y^2 = z^2
\]
The paralogisms of practical reason are what first give rise to the architectonic of practical reason.
Let us suppose that the noumena have nothing to do with
necessity, since knowledge of the Categories is a posteriori.
\end{frame}
\begin{frame}{\textbackslash centering}
As any dedicated reader can clearly see, the ideal of practical
reason is a representation of the things in themselves
{\centering
BEGINNING CENTERING. I have shown elsewhere, the phenomena should only be used as a canon for our understanding.
The paralogisms of practical reason are what first give rise to the architectonic of practical reason. ENDING CENTERING.
}
Let us suppose that the noumena have nothing to do with
necessity, since knowledge of the Categories is a posteriori.
\end{frame}
\begin{frame}{center Environment (extra space before/after env)}
As any dedicated reader can clearly see, the ideal of practical
reason is a representation of the things in themselves
\begin{center}
BEGINNING \{CENTER\}. I have shown elsewhere, the phenomena should only be used as a canon for our understanding.
The paralogisms of practical reason are what first give rise to the architectonic of practical reason. ENDING \{CENTER\}.
\end{center}
Let us suppose that the noumena have nothing to do with
necessity, since knowledge of the Categories is a posteriori.
\end{frame}
\begin{frame}{itemize environment}
As any dedicated reader can clearly see, the Ideal of practical reason is a representation of the things in themselves.
Begin itemize now
\begin{itemize}
\item[$\bullet$] I have shown elsewhere, the phenomena should only be used as a canon for our understanding.
\item The paralogisms of practical reason are what first give rise to the architectonic of practical reason.
\end{itemize}
Let us suppose that the noumena have nothing to do with
necessity, since knowledge of the Categories is a posteriori.
\end{frame}
\begin{frame}{columns environment}
I have shown elsewhere, the phenomena should only be used as a canon for our understanding.
\columnskip 2ex%
\begin{columns}[totalwidth=\linewidth]
\begin{column}{.5\linewidth}
xxx
yyy
zzz
\end{column}
\begin{column}{.5\linewidth}
qqq
rrr
\end{column}
\end{columns}
The paralogisms of practical reason are what first give rise to the architectonic of practical reason.
Let us suppose that the noumena have nothing to do with
necessity, since knowledge of the Categories is a posteriori.
\end{frame}
\end{document}
Best Answer
The syntax of
\multiincludeshould be\multiinclude[<+>][format=png,start=2]{...}instead of\multiinclude[<+>]{format=pdf,start=2}{...}. With this syntax the animation starts with the second image: