What is wrong with making few Manipulates, export them each to separate CDF, and you got your presentation there.
You can make a web page, each page can be contain one CDF. Each page will be like your one slide.
You can click a link to go to the next web page.next slide, and in it you can run the next CDF.
To insert a CDF into a web page, is very simple, like this
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<HTML>
<BODY >
<p><script src="http://www.wolfram.com/cdf-player/plugin/v1.0/cdfplugin.js"
type="text/javascript"></script><script type="text/javascript">// <![CDATA[
var cdf = new cdf_plugin();
cdf.addCDFObject("source", "source.cdf",840,670);
// ]]></script>
<img id="source" src="screen_shot.png"
alt="screen_shot" />
</BODY>
</HTML>
Put your cdf files in the same folder.
If you know latex, you can write latex document, make them as sections of a document, insert the HTML code in latex, export the latex document to html using latex2html. (this is what I do with my web pages). Like this
\documentclass[12pt]{article}
\usepackage{graphicx}
\usepackage{html}
\begin{document}
\begin{rawhtml}
<p><script src="http://www.wolfram.com/cdf-player/plugin/v1.0/cdfplugin.js"
type="text/javascript"></script><script type="text/javascript">// <![CDATA[
var cdf = new cdf_plugin();
cdf.addCDFObject("source", "source.cdf",840,670);
// ]]></script>
<img id="source" src="screen_shot.png"
alt="screen_shot" />
\end{rawhtml}
\end{document}
Then type latex2html foo.tex and that will generate the html for you. This way you can write real mathematics using Latex, and have the CDF in the same page we well, next to your equations.
All what you need for your presentation is a browser and the CDF plugin installed.
Or, you can simply keep everything in Mathematica itself, with a Manipulate in each section of a mathematica notebook, and just run the notebook inside Mathematica at the presentation.
Forget about power points and PDF's. That is so boring and old fashioned now :)
CDF is the way to go.