So why couldn't Apple use those extra lanes on the 13"?
The dGPU uses most likely uses x8 PCIe lanes, as it has in the past (check your System Profiler; under Graphics), which leaves x8 more lanes for TB3 (2 Alpine Ridge controllers @ x4 lanes each). This exhausts the CPU lanes. There are x16 PCIe 3.0 lanes in the QM170/HM170 chipset and Apple needs at least x4 lanes for the SSD/Flash, which leaves 12 for the rest of the various I/O in the system.
This thread has exploded rather quickly. I think the 12 CPU lanes from the 13" Macbook Pros are used for the Thunderbolt Ports, hence the reason why the quad core chips with 16 lanes have the 4 full speed ones.
I've mentioned elsewhere in this thread that I think the new machines will need an Ifixit teardown and some analysis from Anandtech to show how Apple have done what they did to provoke the tech note which has lit the blue touch paper on this thread.
My own speculation is that you need one Alpine Ridge Thunderbolt 3/USB-C controller for every 4 PCIe lanes you intend to present as a Thunderbolt 3/USB-C port. Apple have therefore provided 4 for the Macbook Pro 15" and 3 for the 13" models.
They wanted to have 4 physical ports on 2 of the 3 Macbook Pro 13" models so I think they wired up 2 ports to the one controller handling the right hand side of the 13" Macbook Pro. I think they SHARE bandwidth rather than have a fixed 2 lanes each so you might get full speed if you use one for high performance external storage and the other one solely for charging. If there was high performance SSD storage on both right side ports I took the Apple support document to mean that both would be sharing the total bandwidth available off the single controller and you might get a bottleneck. In the real world, I wouldn't expect simple peripherals plugged in on the right side to drag performance down.
In other words, plug your charger in one of the right side ports and you'll probably not notice any speed drop.
This thread wouldn't be here if Apple had instead chosen to put 3 Thunderbolt 3/USB-C ports on ALL the 13" models and called it a day.
I agree with Zdigit2015 about the chipset PCIe lanes, of which there are up to 16 available on the QM170/HM170 chipset (as per Intel's ARK site). Apple's engineers have therefore given up
8x PCIe lanes for the Radeon Pro RX460 GPU (and presumably the 450 and 455), 4x PCIe lanes for the SSD, and you can bet they'll have split the remaining lanes up to feed the trackpad, toolbar, wifi and camera.
That sorts out the 15" model very nicely.
You have to ask in engineering terms why the 13" model, which doesn't have a GPU to use 8x lanes on, would then go out the door with either 2 or 4 ports depending on which one you buy.
Do you think it might be for aesthetic and/or marketing reasons?
I think most of the emotion being expended here is because prices have gone through the roof and 'innovation' seems a little lacking especially when Apple launch a day after Microsoft. What a contrast.
Somewhere in Apple the engineering department there was a bodge when they designed the Mac Pro and picked an expensive
Xeon CPU capable of providing 40 PCIe lanes, gave the dual GPUs 16 lanes each when one of them spends most of its life just driving a display and the other one is supposedly on compute duties but there's not much software around that would tax it. They then use a SINGLE PCIe lane to drive 4 USB 3.0 ports (which if you hang lots of high performance external drives off them would be a bottleneck similar to what's been mooted earlier in this post).
That's slower than USB ports in a Macbook Pro from 2013.
It just seems to me that there's things in a 2013 Mac Pro that are given more lanes than they deserve, while other functions could be bottlenecked unnecessarily.
Going very slightly off topic, while we are discussing PCIe lanes, we could see the next Mac Pro using the Intel C236 chipset which offers 20 PCIe 3.0 lanes on the chipset (up from the 8 used in the existing Mac Pro chipset). It might allow Apple to engineer a lower cost Mac Pro by boxing clever with a nice CPU/GPU combination.
Pick a Skylake Xeon E3V5 with 16 lanes, direct all 16 lanes to a single top class GPU. Or if the cooling solution demands 2 GPUs then split it into 2x8 PCIe lanes and go with efficient low end AMD ones for compute and wait for the inevitable grumbles. Bear in mind that for most GPUs 16 PCIe lanes is extravagant and unless Apple are using a really powerful one, then 8 lanes ought to suffice for most GPUs if Apple need extra connectivity.
From the 20 lanes available on the C236 chipset:
Use 12 PCIe lanes on the chipset to provide 3 Thunderbolt 3/USB-C connectors (allowing each to connect to a monitor)
Use 1 PCIe lane on the chipset to give us 1 Ethernet port
Use 1 PCIe lane on the chipset to give us fast wifi
Use 2 PCIe lanes on the chipset to give us 4 USB3 ports which aren't bottlenecked
Use 4 PCIe lanes on the chipset to provide fast SSD
The resulting Mac Pro ought to make a very respectable entry level machine. Better yet if you can strike a deal for an i7 CPU instead and gain economies of scale with the iMac. Such a solution would probably still draw moans about the price but if it could slip in at under £1999 it might be food for thought for some.