Your problem is your workflow. You shouldn't ever open PDF files for editing in Illustrator unless it is absolutely necessary. The exploded layers problem you are encountering is just the way that the PDF format is—as the format is NOT intended to be edited.
Your workflow needs to be modified so that both teams are using either InDesign or Illustrator, not both. As for PDFs, they should be used for final documents, or for proofs, never to transport production files.
On behalf of Adobe Systems Incorporated ...
Please understand that Adobe Illustrator is not, repeat not, repeat yet again NOT a general purpose PDF file editor. Adobe Illustrator is only capable of fully editing a PDF file that was saved directly from either the same or earlier version of Adobe Illustrator and if the option was selected to retain Illustrator editability! (Likewise, Adobe Illustrator is not a general purpose PostScript or EPS file editor.)
Thus, you should expect problems when attempting to edit a PDF file exported from Adobe InDesign or for that matter, almost any other program. Why not simply open the Windows' users InDesign documents on your Macintosh in InDesign? That would eliminate all the issues you have.
This doesn't help you with your current workflow, but you might find this thread useful, which includes an AppleScript that moves an InDesign page's layers into a layered Photoshop file (see #85 for the current script).
Posts 78-82 are relevant to your complex layer problem. The script only exports the primary ID layers, which might be what you need. Your designers would need to run the script and deliver the layered PS file to you.
I could pile on here about your workflow but that’s already been taken care of. These InDesign folks should be supplying you with HTML exported from InDesign.
If they properly map their styles to tags you’d have perfectly clean HTML to work with.
Thank you all for your replies. I've been on the 'net since 1994, long enough to know when subject-matter experts are telling me our approach it moronic.
The workflow was set before I started working here; I am unaware how it was decided. InDesign to InDesign would be problematic due to cross-platform font issues. Ultimately we want the designs to wind up in Photoshop (Illustrator was just a waypoint, to extract elements like backgrounds and buttons), so we can slice them as needed. As such, I will see if our designers will give Rob's script a shot.
Are there any other suggestions along those lines?
I agree with the Photoshop workflow. Any website design is handled much easier and better from starting and finishing in Photoshop. you can still use InDesign and Illustrator to create the buttons and import files as smart objects but that's the extent of it.
I don't know what your full workflow involves but what I used to do as a designer sending web designs to a developer and to management for approval was to use InDesign as a way of showing a 'working' sample of the website before it was in development. I basically exported each screen as a jpeg, imported into InDesign and then used InDesign's buttons and interactivity to create a PDF that they could click through and show the functions. I also used InDesign to create the style guide to send to the developer which they told me made their life much much easier.
Some food for thought.
The script is pretty popular for this kind of thing—the thread has 33,000 hits. It doesn't export live text or sub layers.