PDF layers are part of an overall feature known as optional content in PDF and are conceptually very different than Illustrator layers. Since PDF optional content features in general are very much a superset of Illustrator layers (PDFMaker for PowerPoint uses optional content to handle certain slide build features, for example), there would be no easy way for Illustrator to readily pick and choose what optional content features to support and translate. As such, don't expect this to be "rectified" in any way in future Illustrator releases.
(To make things even more interesting, both PDF and Illustrator layers are very different than Photoshop layers which allow for defined interactions between layers such as masking!)
- Dov