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:
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:
And some discussion on regular PDF layer support: