InDesign --> Illustrator, For a Web Design Workflow

I know we can't be the only team that has grappled with this problem, so here goes:

I work for a company with a graphic design department and a web development team; I am part of the latter. Our graphics team works on Macs using InDesign CS5.5 and their designs come to us in PDF 1.5 (Acrobat 6). The development team uses CS5.5 on Windows. The designers primarily output for print (we do a lot of direct mail), so just about everything is geared for that; they also develop our web layouts, which is how we come to our problem...

When we open graphics' PDF in Illustrator, to isolate say, a background, all the text has exploded into 100+ layers making it difficult to track down all the assets we need for the website. One line of text with a stroke around the letters and a drop-shadow behind all that might look like this:

Layer 1

<Group>

T

S

E

B

HE

T                         (THE BEST, displays on one line)

<group>

<clipping path>

<path>                       (stroke)

<compound path>     (stroke again, not sure why this one is different)

.....

..... (more below)

.....

..... (and eventually...)

.....

<group>                              (drop-shadow group)

See how unruly the layers are?

Is this an InDesign issue, say, how they've set up the file? Or an Illustrator problem, interpreting how it's exported? We've done a lot of web research the past couple of days; we're still scratching our heads, trying to isolate the problem, and improve the current workflow. We tried exporting EPS (level 3) and encountered the same myriad-layers problem.

I really, really hope we're not the only ones with this problem and that someone out there has seen it and beat it. Any help would sure be appreciated!

Regards,

Ansel Taft