Some of these are rather obvious - like the first one.. I don't understand how they managed to let that slip through the design process. This makes using the phone while it's sitting on a table very uncomfortable (something I'd like to do when I'm for example eating)

However, I find 5 and 13 to be conflicting. I can't speak for you, but I'm much more likely to be using the phone function with headphones attached than charger (nearly always charging during the night), and the headphone wire would be just as much in the way when talking on the phone. It's also much more natural to put the phone in my pocket "upside down", with the headphone jack staying on top - this way when I take it out it's instantly the right way in my hand. This also ensures the proximity sensor keeps the screen locked as long as it's in my pocket when receiving a call instead of opening it as soon as it peeks out.

To me the best configuration would probably be both connections at the bottom, but this is where limited space comes in.