I agree that there isn't necessarily a need for 3 thunderbolt controllers and 6 USB-C ports. I think the rationale for 3 controllers and 6 ports with shared bandwidth is simply because the ports share double duty with displayport. On the current mac pro, if you want to run 3 displayport monitors, that leaves you with 3 TB ports and 2 TB controllers for peripherals.
Sigh.... how thunderbolt does and doesn't work has been covered multiple times in this thread. You can saturate the PCIe feed to a TB controller by using just one of the two ports that a single controller provisions. What you are implicitly assuming is that users will cover two TB ports from a single controller with two DisplayPort (and/or two USB 3.0 Type C for TB v3). They don't have to. If tip-toe just the right way and take measure of how everyting is hooked up inside. But that is not particularly plug-and-play Apple style. Stretching to three 4K monitors you have to do a bit of that now, but adding in the additional multiple dimensions of the shared USB 3.0 controllers inside the TB controller and displayport and oversubscribed PLX switch. You shouldn't have to look at an internal circuit diagram to pick out what port to plug into. That throws "one plug to rule them all" out the windows when it comes to improving simplicity.
However, I don't see Apple offering USB-C and miniDP on the same machine. I can't think of a case where Apple has increased the variety of ports.
MBP has miniDisplayPort and HDMI when used to just have whatever single video solution Apple was rolling with before Thunderbolt came along. Thunderbolt has been the "more than one" option since it appeared.
What I don't see Apple doing short term is "plain" USB 3.0 Type C and Thunderbolt v3 flavored Type C on the same system. It is the same physical plug but they have different ranges. Apple has avoid that. They went all USB 3.0 instead of mixing matching USB 2.0 / USB 3.0 with different colors.
Apple has also gone FW400 and FW800 for a while on a single system during the Firewire's evolution.
2008 Mac Pro https://support.apple.com/kb/SP11?viewlocale=en_US&locale=en_US
2007 MBP https://support.apple.com/kb/SP13?viewlocale=en_US&locale=en_US
It would not be unusual or unprecedented at all. It is not going to buy Apple many friend to have those limited set of folks who did may the TB v1-v2 investment to have to run out and buy even more dongles. Honestly it is a bit pretty. Even more so when the Xeon E5 v4 + 612 chipset isn't quite ready to an increase of both SSD and TB v3 at the same time. The timing is off to do both at the same time.
Since we already have USB-C on the macbook, I foresee USB-C becoming standard across the line, with everything above the macbook getting USB-C/TB3, replacing miniDP and the magsafe connector.
There is zero rational need for that where there actually is space on the connector panel edge. Dumping all of the 1-2 USB ports into Type-C. Sure. That makes sense because there are just room for those two. But when there are 10+ ports why trying to push them into just one type. With limited space there is added value in doing more with less. With lots of available space it is just dogma. There is no basic need. Space is available and doable with dramatically less resistance from folks about having to buy dongles.
There no good reason to replace magsafe on a 15" or 13" Macbook. The only reason the Macbook goes down to one is the depth is so short which is driven by the sub 13" screen coupled to maximum thinness. (keeping the physical audio jack is another minor point). A very reasonable upper/lower bezel addition and it would work ( the weight savings ouldn't be quite as high though) With a 13" screen (since screen is taller and hence system has to be deeper) there room for 2-3 ports of which magsafe is one. A super light laptop should drop the utility of Magsafe because the laptop is so light it won't detach quickly enough. For a device the size of the Mac Pro it is in the utterly ridiculous zone that have to maximize socket conservation down to just a handful of ports.