What I mean here is that the new Mac Pro has 3 Thunderbolt 2 controllers, which allow for 3 separate 20Gb/s data streams over 3 separate cables, enabling 3 ultra high speed RAID arrays or OCZ Z-Drives.
Tests using Thunderbolt 1 show that it has no problem reaching 1300 MB/s up or down stream. Thunderbolt 2 combines the up and down stream to allow for twice the speed in one direction at a time, at least through the cable.
This is a good point, upping the cable speed will probably hit PCIe x4 bottlenecks. PCIe x4 lanes typically guarantee at least 2GB/s though.
Personally neither completely love or hate the new MP. Like I said definitely all performance metrics are improved across the board and all of your expandability capabilities are improved across the board. And the machine is a lot more compact which is a good thing.
BUT
If Apple expects Thunderbolt to replace physical PCIe slots then they need to support the standard better. Being an early adopter of Thunderbolt 1 for PCIe cards I would call the experience user hostile to initially set up. All 4 of the pricey top of the line PCIe TB boxes I tried were poorly made with tolerances that were pretty embarrassing. Their layouts were incredibly poorly thought out because the boxes used up way too much space for what they needed to do usually having more than 50% empty space despite having unreasonably limited space for the actual card (such as requiring custom low profile PCIe 8 pin power connector or having parts interfering with heat sinks), the PCIe boxes available were physically ugly, and their internal air flow amplified noise, the boxes were literally crooked sometimes and looked like they were put together in a shed out of cases that were never designed for the task they were trying to do, which is probably close to what was going on. On top of that the power supplies were loud and underpowered. You can get power supplies half as large, half as loud and 4 times as powerful for less than $40. And finally the PCIe boxes were hugely price gouged, 400%-800%. The realities of PCIe over thunderbolt are that it's kind of just cobbled together it can work great but getting it working is a rough job.
And that's before we consider the OSX and bootcamp driver support or lack there of. eGPU support through windows 8 is literally there by accident, which is one of the most demanded features with Thunderbolt on Macs.
So if Apple wants to push Thunderbolt instead of PCIe slots they really need to make their own plastic or aluminum rectangle with rounded corners that fits full length full size double wide PCIe x16 cards and provides 250w of power with no wasted space, and sell it at minimal mark up (less than $250) and give the aftermarket a baseline to compete and improve quality control and lower prices, because it's not very good right now and by the time it is good enough, Apple will have lost way more customer revenue through lost lifetime customers than the very minor savings of farming out accessory development gained them.
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