I disagree. Thunderbolt has been adopted very well for what PCIe has always been used for (i.e. serious audio & video I/O, SAS/Fibre adapters, etc.) with GPUs as the exception. That said, I agree that Apple should have prioritised eGPU support, but their whole pitch on the Mac Pro 2013 was that it had dual GPUs already.
In all honesty, the only real issues with the current Mac Pro is: it can't have dual CPUs, and it can't have a big honking GPU and said GPU can't be upgraded after the fact. If they fix those two things, while adding Thunderbolt 3, I think they'll have a hit on their hands. Apparently there are some cases that are effectively small PCs with 1 fast PCIe for GPU. I reckon that'd be a great new Mac Pro (as long as it had everything the current Mac Pro has, plus TB3 and 1x PCIe double width slot and good cooling/power for GPU).
I do think that eGPU support launched with the new MacBook Pros & Thunderbolt 3 would have been appropriate though. I would not be surprised if it's announced at WWDC as a 10.13 feature.
True - but I think it's more the design ideology than designers having power per se. i.e. Apple are obsessed with 'thin and light' these days, which compromises the possibilities rather more than 'designers making it pretty' does. The old MacBook Pros were still pretty, but expandable.