I have recently (perhaps since Mathematica Version 10?) encountered a change in how PDF images are saved and how they behave after being loaded into Adobe Illustrator (v16.0.4 under Mac OS X 10.10.5).
In short: for 2D graphics, Illustrator can edit the graphics--all elements are accessible. For 3D graphics, some rasterization of the graphics is all that is in the exported PDF, and so individual elements cannot be edited in Illustrator.
Here are examples. First, simple 2D graphics:
g = Graphics[
Line[{{0, 0}, {1, 1}, {0, 1}}]]
Export from Mathematica to PDF. Open in Illustrator. (Or just copy the graphic from Mathematica and paste into Illustrator.) Then the elements can be edited. Here is a snapshot from Illustrator:

Now, 3D graphics:
g = Graphics3D[
Polygon[{{0, 0, 0}, {1, 1, 0}, {1, 1, 1/2}}]
,Boxed -> False];
Export["PDFTestExport.pdf", g, "PDF"]
This is what it looks like within Mathematica:

Opening the exported PDF in Illustrator reads in a rasterization, as this snapshot in Illustrator shows:

I tried following @Szabolcs suggestion in another thread to use Preview to resave the PDF, but this didn't change matters.
I certainly used to be able to even copy from 3D Mathematica graphics, and paste into Illustrator, with full ability to edit the elements in Illustrator. So something has changed as various software has progressed through newer versions (Mathematica, Illustrator, Mac OS X). I would love the regain that useful editing capability. If anyone has ideas, I would appreciate hearing them.
(Incidentally, exporting to EPS is not a solution: All such files crash my version of Illustrator upon opening.)