What's the good thinking on Apple's part? Being compatible with USB3 by copying the mechanism that MHL uses to connect microUSB connectors to HDMI and DP?
It's good thinking building a completely generic connector that doesn't adhere to only one standard. So that if <insert new standard> comes on the market Apple could support it without a change of connector.
Apple's connector isn't going to automatically support any signaling they decide to add in the future either. It has to have the proper transceiver in the device as well. If they do decide to add new signaling formats, they'll end up with the issue of newer devices supporting them and older ones not supporting them, which will be rather confusing. The same problem currently exists with HDMI/DP signaling over MicroUSB, though.
The bottom line is that they could have done this just the same with a USB port. In my opinion, all they really got out of designing their own connector was: a) something they can license, control, and collect royalties on; b) a connector that's slightly easier to use (the ability to plug the cable in either way, etc.).
Honestly, I don't think that's their reason for choosing something proprietary over usb. I doubt their first priority was to create something so that they can license, control, and collect royalties on -- if that was their motivation, they would be doing that to the audio jack too. After 10 years of their 30 pin connector, I'm sure they've collected a good amount input from manufacturers & users and engineered something to fulfill those requirements.
I feel like people tend to have these same knee-jerk reactions to anything Apple-designed; they always feel it was designed for the purposes of collecting royalties because Apple is "evil".
I think it's a bit too early to tell if the device connector will lead to confusion over "old" and "new" lightning supported devices considering nobody has released any lightning devices yet. Your FUD is based on existing intermixed standards that have nothing to do with a connector design created by a single company.
