Welcome to Apple Support Communities
If you want to save the file as a PowerPoint, then you have to export it. Go to File menu (on the menu bar) > Export, and choose the PowerPoint format, so the presentation you created will be saved as a PowerPoint file.
Respecting to Save As, it's hidden in OS X Mountain Lion. To show it, go to File menu (on the menu bar) and hold the Option (Alt) key, so you will see how the Duplicate option will turn into Save As