I'm sorry if I sounded harsh or anything, or trying to find false faults in your arguments. That was not my intent, and if you have any backed up information to contradict me, I'd be more than happy to read it.
But, when you look at the dock pinout (
http://pinouts.ru/PortableDevices/ipod_pinout.shtml I know, it's not an official document and does not states anything about the 3GS, but it's still interesting to have a look to) there are a few things to note:
Pins 3/4 are for audio line-out. Since my 3GS does play music back to the car radio, my guess is they haven't changed.
Pins 11/12/13 are for serial communication. Since my 3GS does support the Apple Accessory Protocol that uses serial communication (it supports remote control from the steering wheel remote controls, does communicate track/album names to the car radio (see pin 21) when the car system is in "Gateway Mode") my guess is that they haven't changed either.
Pin 21 is for accessory indicator. Its the one that triggers the warning message stating that the plugged accessory is incompatible with iPhones, or triggers the "iPod Accessory" mode with serial communication (see pins 11/12/13). Maybe Apple introduced new resisting values to manage 3GS specific accessories, but everything points to the fact that old ones are still supported (as the 3GS goes into "iPod Accessory" mode when the car system is in "Gateway Mode" and communicates correctly track/album names through the Apple Accessory Protocol, or that the volume gets locked into "Dock connection" mode when plugged in, etc.)
Pins 16/23/25/27 for USB charging. Since the 2G/3G USB charging adapters are still working with the 3GS, my guess is that they haven't changed.
Finally, for the 3rd party accessories that don't work as designed or at all going from 2G to 3G to 3GS (such as your BOSE SoundDock), the only issues I'm aware of are the firewire charging issue, and the "accessory not made for iphone" message (which is due to the fact that the accessory has not been shielded for radio interferences, thus not having a resisting value on pin 21 that relates to an designed-for-iPhone accessory). There is also the issue of the chip in the video-out cable, but that concerns the migration from iPod 5G to iPhone, not 3G to 3GS, and my car system isn't video cappable, so it's not applicable here. But If you have any information of other bugs affecting these devices, feel free to point me to them.
That is (AFAIK, again) what happened with the BOSE SoundDock Series I vs Series II : the I was charging via firewire only and had a resisting value on pin 21 that registered it as an iPod accessory (thus the warning message on iPhones, both 2G and 3G), whereas the II has USB charging and a radio frequency shielding, so it is authorized to register itself to an iPhone as an iPhone accessory (different resisting value on pin 21, thus no warning message).
But I guess we're going slightly out of topic here, which is that when my accessory is plugged in (and provides both firewire and usb charging), the iPhone initially detects the usb charging (thus the vibration and charging icon) but soon after loses it as it seems it detects also firewire charging.
One might say that this is due to the 3GS detecting a now-unsupported resisting value on pin 21. But when I use the firewire-to-usb charging adapter (link in my previous post) that passes through signal from the other pins, it then has the same resisting value on pin 21, but now only usb charging (no FW) and does not loses charging as it happened without the adapter. *That's what points me to either a hardware firewire-to-USB power conversion problem, or a software bug in my iPhone.*
Sorry for the long post, I hope I haven't lost you (or an Apple Software/Hardware Engineer reading it).
Have a nice day.