Hmm, for the 15" MBP Apple has an entire separate TB3 controller to allow all the ports to run at high speeds. Could they do something similar for the MacBook to add lanes? The motherboard is so small it's unlikely I guess, but I'm sure Apple would like to do it.
At any rate, seems to me that 2 also makes for a better experience if you want to charge with one and use the other for data at the same time.
Is that right for the 15? If so, I hope it happens. 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.