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You probably have a bitmap symbol or a transparency setting in a layer above the ones being pixelated, because that would rasterize all layers below it in the TOC. You might use ESRI's free Detect Complex Output extension to find out if there is such a layer, or look for it in their symbols or properties. Or you could look in the layers list of your pdf, and see which one is missing, and if it (or others) goes on and off with the pdf's image layer, that's your problem layer(s).
How to get consistent quality of vectors when exporting to AI format
Problem: Polygons are divided in tiny strips when exported to EPS, PDF, CGM, or AI Illustrator
Enable/Disable dicing with VB
Increase vertex limit via windows registry
Modify the vector export polygon vertex limit in Advanced ArcMap Settings
That is if you are having trouble with the vectors in your map. This is called dicing, which by default is set to somewhere around 10000 (different vector formats have their own setting by default), this is like resampling your vectors for quicker on screen display and drawing. Unfortunately, this limit is included in the export to the vector formats as well, but the workarounds above work great.
I often increase the vertex limit (first count the vertices using python):
Parser: Python Expression: MySub(!shape!) Code Block: def MySub(feat): partnum = 0 # Count the number of points in the current multipart feature partcount = feat.partCount pntcount = 0 # Enter while loop for each part in the feature (if a singlepart feature # this will occur only once) # while partnum < partcount: part = feat.getPart(partnum) pnt = part.next() # Enter while loop for each vertex # while pnt: pntcount += 1 pnt = part.next() # If pnt is null, either the part is finished or there is an # interior ring # if not pnt: pnt = part.next() partnum += 1
taken from: Calculate field examples
If you have some troubles, export your layers to PDF or AI format one layer at a time (with a neatline) or group them and export as groups of similar layers. This will help reduce file size.