Still searching and searching for a resolution to this problem. As others have stated, bluetooth is simply unusable (for phone calls, at least).
I've even tried to locate a phone with 3.0.1 with little luck. You can find them on ebay for about $899, and they want an extra $200 for a phone with 3.0.1.
A few things that might be helpful:
-Has anyone tried connecting multiple phones to these Pioneer head units and NOT had the problem with firmware 3.1.x or greater?
-Does anyone have a Pioneer support contact they can share?
-If your phone doesn't work, I think it would be very reasonable to go on to amazon and post a review indicating that your head unit is not compatible with the 3GS - I did.
Any other ideas? The iphone hacking scene has made it very hard to find phones with older firmware, even for very legitimate reasons!