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Converting a PPT to a PDF while maintaining the animation steps is something I too have been looking into for a long while, without finding a satisfactory solution.
That is why I have decided to write an add-in on my own which does exactly this:
splits the slides at each animation step (being it mouse-triggered or not depends on the user's choice) while modifying (adding, deleting, altering) the shapes in the "fragmented slide" according to the animation effects. If you are interested, I have packaged the add-in in an easy-to-use installer, which adds a toolbar (or tab, if you are using Office 2007) to your PowerPoint. In case you are not satisfied, you can easily remove the add-in using the standard Control Panel "Add/Remove Applications" tool.
You can get PPspliT here. Examples of usage are also provided.