Do you have Adobe Acrobat Pro or Standard? In Pro, there are two ways to save a smaller PDF file: You can select the "reduced size PDF" option, but you can also save as an optimized PDF. The second option gives you control over how the file size gets reduced, and, the saving as an optimized PDF can be automated via the Action Wizard. This allows you to select one or more PDF files (or all files in a certain directory) and save them with the same optimizer settings.
Unfortunately, neither saving as an optimized PDF, nor the Action Wizard is available in Acrobat Standard.