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.
You couldn't do that with USB.
You couldn't do that with USB.
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.).
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.