This answer doesn't address your particular beamer problem, but rather discusses the general problem: developing a method for conditionally compiling a source document in two vastly different ways.
We do this with my organization's report stencil. It allows, with the change of a single word, to change from an organizational report, with Covers, mandatory government forms, distribution lists, figures and tables in the text, into a manuscript form that eliminates the cover, cuts out the forms and distribution list, while retaining things like keywords (which were part of the government forms too), with tables and figures collected at the end of the report. Naturally, the margins, fonts, etc. are all different, as well.
The basic structure of the stencil would be something like this, which provides conditional compilation, depending on which of two settings is specified by \PREPARETYPE:
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Choose desired document format HERE!:
\def\PREPARETYPE{\DOCTYPEA}% choices: {\DOCTYPEA} or {\DOCTYPEB}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Set up for possible DOCTYPEA format:
\newcommand\DOCTYPEA{
\documentclass{MyOrgClass}
\usepackage{packages for DOCTYPEA}
\def{settings peculiar to DOCTYPEA}
\macros peculiar to initializing DOCTYPEA
}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Set up for possible DOCTYPEB format:
\newcommand\DOCTYPEB{
\documentclass{article or whatever class is desired for DOCTYPEB}
\usepackage{TYPEA2TYPEB} % <--- ESSENTIAL TO INTERCEPT/INTERPRET MyOrgClass MACROS
\usepackage{packages for DOCTYPEB}
\def{settings peculiar to DOCTYPEB}
\macros peculiar to initializing DOCTYPEB
}
\PREPARETYPE
%...common preamble commands
\begin {document}
%... document text, figures, tables, etc.
\end {document}
The key, however, to making such an arrangement work, is a style you need to develop that, in this MWE, is called TYPEA2TYPEB.sty. In particular, it's sole function is to create macros with the same non-standard names as occur in MyOrgClass and provide the manner in which they should be interpreted by \DOCTYPEB. In many cases, it may be a null definition {}, as would be the case for features of \DOCTYPEA that are eliminated by \DOCTYPEB. In other cases, a new non-null definition must be provided.
While we don't need it for our situation, I suppose one might also need a TYPEB2TYPEA.sty style to be included in the \DOCTYPEA macro definition, if the class employed by \DOCTYPEB also uses non-standard macros.
While this answer does not solve your problem for you, it lays out a method of producing two documents with vastly different formatting, that can be brought about by changing a single word in the source file.
I attach a figure, for what its worth, showing two documents from the same source. On the left is a manuscript form, on the right is an organizational report form. I do this just to emphasize the vastness of difference in results that is possible using this approach.

.texfile, then\input{preamblex}at the start of your document before compiling. Herexis 1 or 2 or a name of your choice. There are more complex ways, using a switch or a command line argument, but this might solve your problem. – Ethan Bolker Aug 12 '13 at 14:43beamerpackage, you can use thehandoutclass option to collapse the overlays (see http://tex.stackexchange.com/q/1423/86) To make them 4-up, usepgfpages(see http://tex.stackexchange.com/a/4775/86). Wrap thepgfpagesuselayoutin\mode<handout>{...}to ensure that it only has effect inhandoutmode. – Andrew Stacey Aug 15 '13 at 18:36\mode<handout>{...}can be used to make even more extensive changes between the presentation and handout modes. I recommend reading the section of the manual that deals with producing different types of output. – Andrew Stacey Aug 15 '13 at 18:38