While I don't copy the layers I want into another document, I hide the layers I don't want to print, then I "Flatten Artwork" in the Layers menu, opting to delete non-visible layers. I then "Save As", and choose PDF. I then close the Illustrator file, so I don't re-save as an Illustrator file and lose all my layers.
I find that Flattening greatly reduces the PDF file size.