On a related topic, Esko have released a "Deskpack PDF import" plugin that maintains layers etc.
NEW! DeskPack PDF Import - Esko
• The layer names are preserved, the locked status is preserved and the printability flag is preserved.
• Named objects: the names of artwork are preserved.
• Inks: EskoArtwork screenings, ink types, ink books, and ink order as shown in Ink Manager are preserved.
• For each object, the EskoArtwork screening is preserved and shown in InkManager. The Screening plug-in is not necessary for this functionality.
• All Structural design layers (from the CAD file) are imported.
• Page boxes: the Media Box and the Trim Box are imported and shown by the Trim Box and Media Box plug-in.
• Text is handled in a better way, text is kept live as much as possible
• Linework with mixed (DeviceN) colors will be converted into multiple appearances instead of resulting in an ‘unknown imaging construct’.
• Linked images: PDF Import supports links to external images. All links are preserved.
• Channel mapped images are recognized and remain their mapping, even on linked images.
Not free though... €400 / seat...