Why can't they just make a JACK connector, with 4 wires, like for the iPod Shuffle? That would allow everything to go through ONE port, it would be easy to manufacture, compatible, and there would be no wrong way of connecting it. Not to mention it's tiny.
You could then replace all the USB, Thunderbolt, FireWire 400, FireWire 800 and all that random stuff with ONE connector that would be easy to connect, cheap to buy and it would be very small and secure.
Wake me up when it will be possible to supply data at high speed and enough power through 4 cables with a jack connector.