Except Apple is already doing something like that with the 13" MBP now. Two of the four ports don't support full bandwidth. And they aren't marked in any way to alleviate the confusion for the user. So your rationale for not including a second port due to confusion, doesn't really measure up based on Apple's current practices. In the end, convenience and portability is the driving force for many who use the MB, and having an extra port would be more of a convenience than not.
https://www.macrumors.com/2016/10/28/macbook-pro-tb3-reduced-pci-express-bandwidth/
Also, should USB-C headphones become an thing, nobody's going to want to carry around a hub just so they can plug their headphones into their MB while they use the port for anything else.
The MacBook Pro 13" is a different situation.
The 4 ports technically do support up to full USB 3.1 specifications at any random time, no matter what is plugged into them. So there is no confusion there. USB-C is technically "at least" USB 3.0/3.1.
On the MacBook, it's different. The 2nd port will drop to USB 2.0 speed as soon as you plug a 4K/60Hz display into the other. Note how other Core M devices on the market (up to Kaby Lake) also do not do things any differently. Some of them do not even sport USB-C, and instead, they sport USB 3.0 along with HDMI, or USB 2.0 along with Mini DisplayPort that may support 4K/60Hz. This is a limitation of the chipset.
Specifically, Core M 5th gen had PCI-E 2.0 data lanes... that was barely enough for 4K/60Hz. Core M 6th gen, on the other hand, has PCI-E 3.0 so it has much more bandwidth at its disposal and could support 4K/60Hz more easily, along with HDMI 2.0. But there still isn't enough bandwidth for more than USB 2.0. If we're going into more technicality, yes, I concede there are devices that sport 2 USB-C ports, one running at full USB 3.1 specs along with delivering DisplayPort, and the other only delivers USB 2.0 speed, and is mostly used for charging, but the problem really is that your layman won't read the manual, so they'll plug their display into the other port and find out it's not capable of outputting to a display. Then a lot of trouble ensues.
This is not the case with the MacBook Pro. All ports can output to an external display, and/or be used with USB 3.0/3.1 devices in any scenario, although only 2 of them can do Thunderbolt 3.
Also USB-C headphones do not exist because there is no standard currently for outputting analog signal with USB-C.
USB-C is controlled by a board of companies rather than just Apple, so Apple cannot just do whatever they want either. This is very unlike the whole Lightning situation since Apple controls Lightning standards.
tl;dr: Kaby Lake is not gonna work magic. See this article for more info:
http://www.pcworld.com/article/3113...-chip-is-a-must-have-for-4k-video-fiends.html