I saw this posted about a year ago (Can QGIS preserve layers when exporting to PDF?) but figured it was worth asking again -- is this possible? My usual workflow with ArcGIS is to export to AI then edit the layers that way, is there some way to do that from QGIS? Now I just get everything in one huge layer. Thanks.
See if this helps with the Illustrator part of your question:
Losing large portions of elevation contours from QGIS to PDF
Short answer on QGIS layers to PDF layers support, not yet. My guess would be some form of support might show up by way of the GDAL/OGR providers.
Sample of Model-Tree (not produced with GDAL/OGR)
The GDAL driver appears to have support for layering an OGR data source over a raster layer (see OGR_DATASOURCE).
Here is some recent discussion on the subject:
GDAL - Dev - [gdal-dev] Geospatial PDF with OGR_DATASOURCE
And some discussion on regular PDF layer support:
GDAL - Dev - [gdal-dev] PDF selective layer sample wanted