We recently bought the new 2013 Honda crv and have been facing the same issues, however, I have gone in dept and found some necessary details. While the phone is connected to the stereo system of my car, when I receive a call and i pick it up from the car, the call gets connected but no conversation is able to happen on both sides. When I unlock the iphone (that is connected to the Bluetooth), I get 3 available audio options to choose - handsfreelink, iPhone, speaker. Currently handsfreelink is active, which it should be, but in order for any sound to go through I have to manually tap the iPhone or speaker option, then reselect the handsfree option. Everything after that works fine.
Now the reason this happens is because the iPhone is currently locked (whether u have a passcode or not). if you're having the same problem as I mentioned above, then try unlocking your iphone that is connected through Bluetooth, then try calling, and when u pick it up from your stereo system everything should work fine w/ out u having to manually tap anything on your phone.
Now there are several possible solutions to this:
1. You could use Cydia or other third party apps to disable your lock screen permanently.
2. You could set the auto lock to "never" in your settings and unlock your phone and leave it on before start driving.
3. You could disable incoming calls or put them on silent while the phone is locked. I don't know how to do this, but it is possible.
To be honest I don't like any of the options above. I have disabled the phone from my car and will not be using Bluetooth until a real solution is found by apple. I did call apple as well and they said they might be thinking on this for the next upgrade (could take several months) if it is requested by enough users.
Good luck and keep me posted
Abhi