This has already been touched on a bit, but I wanted to highlight/clarify that layers in your table of contents that are below the set transparent layer will be lumped into the PDF raster.
To reduce the number of layers that become pixelated in your PDF slide the transparent layer as far down as possible in the table of contents in the mxd prior to exporting to PDF.
(just my two cents)
On a similar note, The issue I'm coming across is that I would like to create a layered PDF (for Adobe Acrobat Pro) where I can turn on and off the transparent layer ONLY. To my knowledge it does not seem possible. The best idea I could come up with was to try overlaying a new data frame of the same extent and size over the main data frame. This new data frame would be at the top of the table of contents and only house the transparent layer. However, when I tried this the "transparent" layer did not display the imagery from the other data frame behind it, so the effect was just a lighter solid color for the intended transparent layer. So, I gave up...
It would be a great feature to be able to overlay data frames with the same functionality as a layer. (Maybe something to add to the overstuffed suggestion box)