So how long before Thunderbolt and Lightning are both replaced by USB-C?
Port convergence is a good thing in the long run, but it does seem like a bit of a slap in the face after they just finished pushing everyone towards their proprietary(-ish) standards.
Will TB be replaced by USB-C? Yeah, providing the push to 4K outstrips Thunderbolt's ability to daisychain displays.
Lightning? Probably not, mid term. Lightning is still smaller and Apple owns the standard. I don't think Apple would switch unless Lightning reaches an end-of-road tech position (like, if they really wanted iOS devices to have USB/TB support, or if they needed a lot more bandwidth and just couldn't get it). "A slap to the face" isn't necessarily wrong, but it's pretty easy to see how Apple themselves pushed the USB forum into these upgrades.
In any case, it's the future, but it's the "limited production" future. No other USBC devices exist right now. I'm sure their ability to manufacture is pretty limited. That will open up later as the PC market gets in on the action, but for now they can charge what they want because nobody else is pumping out USBC devices and platforms. That's why you don't see the 13" MBPR with these ports - Apple is letting the NMB ride the future wave while everything else waits on the market to catch up.