To each their own I guess. I bet if you tried it for a day, it would start to feel natural. I like being able to withdraw my phone and use it immediately. The headphone port on the bottom would be perfect for me.
Either way, if you've ever plugged in the dock connector wire and a headphone wire at the same time, you'd know how annoying having wires on both sides of the phone is (which is my current car setup). It's worth changing just for that reason in my opinion.
What if the phone is docked but you still want to listen to music via headphone?