I think there's a fundamental misunderstanding about most of the compalints about the new Mac Pro.
Before we begin though let's address the cost, thunderbolt expansion is expensive because it's new not because it's expensive to make. I own an Sonnet Echo Express Pro, that cost me upwards of $700. The parts that go into it are marked up over 800% and the market will tank in price very quickly considering you can buy the pcie to thunderbolt controllers for $80 right now, but Intel won't let consumers buy them, only manufacturers.
The first thing to understand about Apple's New Mac Pro is that it had to have a single processor, the chipset only supported a single processor at this time with thunderbolt, so if Apple wanted thunderbolt they had to go with a single processor. However you can have up to 6 external Xeon Phi co-processors, and the single processor has as many cores and is faster than the dual processors it replaces.
Second, Apple had to go with Firepros instead of Nvidia cards, AMD is far less interested in marking up their workstation cards, and sure you don't get CUDA core support, but if you did then you'd be paying $2000 more for the machine. Instead now you can have both the internal GPUs and up to SIX external ones. I've attatched a GeForce Titan with a PCIe to Thunderbolt adapter and VisionTek 3.5" 450w stand alone power supply to practically every Mac that Apple makes that has thunderbolt and it works extremely well. If you're actualy running applications that need CUDA cores, having 6 external cards sold at market price is a huge blessing, over 2 internal ones that are sold at a mark up.
Third, external PCI cards, external hard drives, and external optical drives are the way of the future. Why?
Flexibility:
Image
The last generation Mac Pro had to make an educated guess on how much EMPTY space you needed, and when you were done using that empty space, there was NOTHING that you could do to expand it without an engineering degree and a manufacturing plant. Apple had to guess that you needed 4 PCIe slots, if you needed 5, well too bad, and if you didn't need those slots you were wasting space.
The new Mac Pro does away with the guessing game and gives you the option of nearly unlimited expandability. You can have up to 60 PCIe slots now, which is 15 times as many, and up to 300 hard drive arrays or optical drives, which is 75 times, and 150 times more respectivly. And guess what, the Mac Pro is smaller. How is that not revolutionary?
Fourth, the biggest issues of all that has come up. Clutter. Cables, Mess, Junk. Hoestly I think this is a very short sighted issue. If it REALLY bothers you that much, then just buy a recycled Mac Pro case off eBay for $100 and some zip ties you can have all the internal parts you want. However, I haven't heard of a Mac Mini or an iMac user complaining, and guess what? Companies will come up with neat little solutions to package all of your external devices around the new Mac Pro, and here's the thing, if you ever decide that you need even more room, you won't be SOL, you'll simply buy a new dock or stand for your Mac Pro with more room.
The new Mac Pro is about flexibility and scalability, unlike the last version which was one size fits all that didn't really do a good job at fitting anyone except the exact person who needs 4 hard drives, 2 optical drives and 4 PCI slots exactly.
Image
The Mac Pro is the future of computing.
Finally, the biggest issue of all, performance the new Mac Pro can meet the needs of literally anyone who owned the last generation Mac Pro, every single performance and expandability criteria is higher. Everything you could do with the last model, you can do equally or better with the new one.
Image
You'll notice that not only are all performance metrics improved across the board, all of your expandability capabilities are improved across the board. Instead of having 2 PCIe 2.0 x16 slots used normally for the graphics cards, you have 2 PCIe 3.0 x16 slots used normally for graphics. Instead of 4 PCIe 2.0 lanes for expandability (shared between slots 3 & 4) you have 3 PCIe 2.0 lanes shared between 6 thunderbolt cables. That's 3 times the expandability before we consider daisy chaining, and you can use full x16 cards at x4 speeds just like before. On top of that there are several Mini PCIe connectors internally, not to mention USB 3.0.