Well, after much testing and talking to the Apple engineers I have an update for you all.
1. all iPhones with OS3 work completely with the Pioneer F series
2. all iPhones (including the 3GS) will charge when connected ****caveats below
a. iPhone 3GS REQUIRES currently available Apple branded AV cables (PIONEER cables are NOT compatible with charging the 3GS)
b. using an additional USB extender cable KILLS charging capability (for the 3GS)
I found upon testing that adding a USB extender cable (Belkin, GE, and others) somehow kills the charging capability of the iPhone 3GS, but not the first generation or the 3G. This was tested at the headunit itself. However if you plug the AV cable directly into the headunit (without extender) the iPhone 3GS charges fine. This however is NOT the case with the Pioneer branded cable - it will not charge the iPhone 3GS at all in any configuration.
All other current iPods and iPhones including the 3G do CHARGE and operate correctly regardless of the iPhone OS.
in case you are wondering I have tested this myself in "real world" conditions and have conferred with Apple regarding this issue.
I have noticed on some F series decks that a reset on the headunit is required after the OS3 update for the iPhone and iPod. This is a random, unduplicateable issue.
Please feel free to PM me with any questions or comments......
Clark