The old dock connector, and the new "lightning" connector do a lot more that is supported by a USB connector. The dock can carry audio, video, act as a USB slave, and connect other slave devices.
Arguably, Apple could have included both ports, but that increases cost and complexity and flies in the face of the Apple aesthetic.
They could have AT LEAST gone with USB3. I mean really, it's 2012 and you release 'the most advanced phone ever' and it's running technology that's 10 years old. It's not as if better, "standard" options don't exist.
I'm looking forward to the day wireless just works, but I'm not sure we're any where near close yet. I still have a problem with my WiFi dropping because next door is using theirs, and that's after I picked the least congested channel.