I'm optimistic that between Apple's recent use of USB-C on the MacBook and its past embrace of Thunderbolt, we will begin to see Thunderbolt 3 ports on future Macs. While it's possible that Apple will turn its back on Intel and Thunderbolt, this announcement feels like the sort of technology Apple would want to integrate into its future products, since it joins USB and Thunderbolt into a single port and provides all the versatility that Apple needs. It's easy for me to imagine these ports replacing all the existing USB and Thunderbolt ports on future Macs.
And now the caveats
If Apple makes a major port transition — no matter if it's to standard USB-C or to Thunderbolt 3 in a USB-C wrapper — it'll mean that Mac users will enter a frustrating period of inconsistency. We'll all be buying adapters for old products and getting frustrated that our current Mac doesn't support some whizzy device that only supports USB-C or Thunderbolt.
If Apple does adopt Thunderbolt 3 across its product line over the next year, this could mean that this year's 12-inch MacBook might end up as a bit of an oddity. Not only does it have the one port, which is odd enough, but it might be one of the few Macs to have a plain USB-C port rather than a fancier Thunderbolt 3 port.
There's also the issue of driving 5K displays. Intel's announcements about Thunderbolt 3 mention that it supports DisplayPort 1.2, which can drive high-resolution displays, but doesn't appear to have enough bandwidth to drive a 5K display via a single connection. (It can definitely do it via two cables.) The new DisplayPort 1.3 specification, which is being finalized, is supposed to support 5K displays via a single cable. It would be silly if a brand-new technology like Thunderbolt 3 shipped without the ability to drive 5K displays via a single cable, but that might be the case. We'll have to wait and see.
Finally, there's one other catch about Thunderbolt 3 adopting the USB-C connector: Room for confusion. You should be able to plug any USB-C device into a Thunderbolt 3 port without trouble. But if you've got a computer (like the new MacBook) that supports USB-C but not Thunderbolt, Thunderbolt peripherals (indicated by the lightning-bolt Thunderbolt logo rather than the USB logo) just won't work (even though you can plug them in).
In practice, I'm not sure this will be a huge problem. Most hard drives and other simple peripherals will probably just use USB-C in order to maximize compatibility. But some devices, including docks, will require Thunderbolt, and those won't work on USB-C-only devices like the new MacBook.
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