At some point, PCIe v4.0 (or 5.0, depending on how you read the tea leaves), is going to be a thing. Given that it increases bandwidth 2x over PCIe v3.0, I suspect that once a version of Thunderbolt that runs over PCIe v4.0 is released (not anytime soon), all of these complaints tend to just wither away. Apple runs mobile GPUs at x8 in its 15" MacBook Pros and has for years. I am somewhat surprised that a dual-cable x8 solution using 2 Thunderbolt port (1 from each controller) has not surfaced, unless the fundamental design of Thunderbolt makes this implausible. IANAEE, so I would defer to someone who is more qualified to talk about the subject. Given the complex nature of what a GPU does, I supposed splitting the signal at one end and rejoining at another is a particularly insane and very tiny use-case, regardless.
So, once PCIe v4.0 is supported and shipping, it makes things a bit easier from a bandwidth perspective once a successor to Thunderbolt 3 is released. The timeframe is the sticky subject now.
I do not think everyone is hung up on internal expansion, but there are quite a few use cases where it is less than desirable. One fairly important use case exists in the creative community. For many, the 2006-2012 Mac Pro (but especially the 2009-2012 models), made it easy to have this super powerful computer complete with storage, DRAM, GPU, any special case PCIe cards, etc. completely self-contained and easily, quickly packable into a single Pelican hard case that could be shipped anywhere in the world, and as long as it arrived, you were golden. Whether you are a musician, a film maker, a photographer or an engineer arriving onsite to work on something that needed you there, you had the horsepower to pull off the job and not try to keep track of more than one or two boxes, the Mac Pro and the monitor you were using. In all but the most remote locations, you can usually scrounge up a USB keyboard and a mouse, although if you forgot to pack it with the Mac Pro, you need a timeout. A monitor is harder, but still, shipping multiple boxes can result in exponential stress if one of those external items is lost. Not to impugn logistics and shipping people around the world, but I swear the more boxes you add in a single shipment, the hairier things get.
Truth be told, I have had my share of expandable Macs dating back to 1991 and I rarely ever needed to install a NuBus, PCI, AGP or PCIe card in any of them. I moved to an iMac and MacBook Pro combo and have not needed anything more powerful than a Core i7, but if you do need those cores AND an NVIDIA card, and a 10Gbps Ethernet card and, say, a Red Rocket card or a SAS PCIe card, after a while it gets a little disheartening to see how much Apple really does not seem to care about you as a user and a customer.
Apple's self imposed exile from the traditional tower form factor gets old...none of the Pros who want would argue that it is an old idea, but none of what Apple has proposed as an alternative has shown them something fundamentally better. It really just shows that Apple thinks it knows what these customers want, but do not.
I honestly think the current 2013 Mac Pro chassis would have made more sense as a consumer desktop companion to the 27" iMac or as a desktop companion to a Late 2013 Mac Pro tower for those Pro users who need more cores, DRAM and GPU power, but in a smaller package than the Pro users who need an all you can eat buffet style of computer.
The flip side being...how much time and engineering that would have taken at the expense of the iPhone, iPad, Apple Watch, AppleTV, MacBook Pro, iMac, MacBook Air, MacBook, et al. that collectively stomp into the ground the revenue generated by Mac Pro sales. Examining it that way, the Pro user will lose every single time, which is a shame, but it is business. Hoping 2019 gives the Pros out there what they are hoping for after a 5 year drought.