I also have 10.11.3 and here's what I did to make this work...
Step 1
go to HD/Applications/Utilities/ColorSync Utility
click the + at the bottom to create a new filter - named it 'Compress PDF'
left click on the circle down arrow on the right side of the window - Add Color Management Component > Convert to Profile
In the drop down select Generic RGB Profile > All Data > All Objects
left click on the circle down arrow on the right side of the window again - Add Image Effects Component > Image Compression
In the drop down select JPEG and move the slider to about 1/4 of the way from the min
Step 2
create a new folder named Filters and place in HD/Library
Step 3
go to HD/Users/Name/Library
if the Library is not visible then it has been hidden -
see http://www.macworld.co.uk/how-to/mac-software/how-show-hidden-files-in-mac-os-x- finder-funter-3520878/
if visible, select the Compress PDF filter and move it HD/Library/Filters
The Compress PDF filter should now be visible at top of the options when saving a file in Preview
Now, can someone show me how to restore Compress PDF in the Print Dialog Box under the PDF options?