I can't really answer as to why it's so inefficient, but i've had the same problem, and i got around it by using free Quartz filters from Jerome Colas.
This post on the Apple discussion boards has the details, but the link is broken, an extra * on the end breaks it, it should be https://public.me.com/jcolas.
Download, unzip, and add the "Filters" folder to your Library folder.
To use, open a PDF in Preview, click File > Save As, then select Quartz Filter, and the level of compression.
I believe that Jerome is exposing something that already exists in OSX, but certainly, it's a good solution that works well for me, allowing me to get a good balance between quality and filesize.