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AnandTech has a great review of the new Mac Pro. The past decade every new model looked virtually identical to the previous one, even when Apple migrated from PowerPC to x86 CPUs. Apple seems to be overcompensating for that stagnation now. The old Mac Pro was the only machine that was still expandable internally: it had tons of room for many drives and PCIe cards. With the new one, you'll have to use the external Thunderbolt and USB ports instead. I think that's not unreasonable for the most part, but the way I see it, the new Mac Pro really needs an internal 10 Gigabit Ethernet (10GE) interface.
Yes, without PCIe slots you can't put any HDMI capture cards and the like in a new Mac Pro. That's annoying right now, but this problem will go away fairly quickly as these applications move to Thunderbolt and/or USB 3. This is a much bigger market anyway, because all of Apple's computers now have Thunderbolt and USB 3.
I can see why Apple wanted to get rid of the drive bays. Those take up a lot of room. Perhaps moving to 2.5" drives rather than the traditional 3.5" ones would have helped, but 3.5" drives are still cheaper for the same capacity, and I assume also faster. Only having two 3.5" drive bays or only 2.5" drive bays would have meant that many Mac Pro users would have had to use some external enclosure for big, fast storage anyway, and this way Apple gets to build a super small system, which seems to be their goal in life.
The AnandTech review shows that using USB 3 for external storage isn't great, as the bandwidth to the USB busses is limited. And of course Thunderbolt is 10 or 20 Gbps while USB 3 is only 5 Gbps. A Thunderbolt-connected RAID array is great if you only have a single Mac Pro, but what if you're a business that has a number of them? Having separate RAID arrays for each Mac Pro is not a great solution: it would be much better to use network-attached storage. But that's not really an option over the Mac Pro's built-in Gigabit Ethernet ports. These only provide 10% of the bandwidth that Thunderbolt provides.
With the older Mac Pros, you'd simply put in a 10GE card. With the new Mac Pro, you have to use one of those cards with a TB-PCIe converter or a TB-10GE adapter. Both solutions require and additional (beefy) power supply.
10GE cards aren't cheap. Perhaps Apple didn't want to increase the cost of the Mac Pro. But as it is right now, it's a typical v1.0 product: amazing in many ways, but lacking one or two crucial features. I hope that in the next iteration, Apple puts in 10 Gigabit Ethernet. A good way to do this would be with an SFP+ interface. Currently, there are many different fiber SFP+ modules, and hopefully there will be UTP SFP+ modules in the future.