In fairness, Thunderbolt isn't that much worse than PCIe; there aren't that many use-cases that really need more than 10Gbps, and even less that need more than 20Gbps. I mean, if we ever get some good, reasonably priced Thunderbolt 2 RAID arrays, they'll be better than the common 2x Mini-SAS options we had before; it'll still suck that you can't just keep using those without a huge premium, but the potential is there for Thunderbolt to provide superior options.
I disagree that TB will uproot MiniSAS (outside of New Mac Pro owners, where TB SAS controllers are $900 for a single port). MiniSAS can actually do a theoretical 24Gbit/s - 6Gbps x 4 channels per port. That is significantly better than TB 2. That's not to mention the fact that a 4-port MiniSAS PCIe controller with a total of ~8GBps of throughput (or 80Gbit/s) costs $450 -- 33% more bandwidth than all the TB ports on the nMP combined. To get even close on the nMP, you would need 3 separate controllers, and the possibility of anything but a software RAID isn't there. Even on the old MP it has huge advantage: After you plug that PCIe card in, you still have 1 slot for your GPU and 2 more 4x 2.0 slots. If you use your expandability primarily for storage, this is huge.
Even if TB2 accessories become ubiquitous, it is simply not efficient to have multiple controllers on multiple cards performing the function of a single controller.
I guess if you don't care about bandwidth, you can run your 8 drive array over a single TB2 port. At that point the comparison is more akin to using PCIe eSATA controller with the addition of port multipliers -- a much, much cheaper solution with similar speeds.
MiniSAS cables are cheaper and are capable of 30 feet, copper Thunderbolt cables can only do 10 feet. Sure, eventually you can get optical thunderbolt (theoretically at least... they've been "about to come out" for 10 months now), but I believe when it was discussed before, rumors were it'll start at $800. A that price point, you might as well compare it to FiberChannel which can do 30 miles.
Besides that, for the more common use-cases for which Thunderbolt is plenty, it's actually better overall as you can use plug-and-play devices compatible with any recent Mac, and you can daisy chain a load of devices together, which are both capabilities that PCIe lacks. The latter is a fairly important capability too, as the previous Mac Pro was severely limited in how many expansion cards you could fit, while the new one take the same number of Thunderbolt devices connected directly, and potentially a lot more using daisy chaining.
All that is definitely true. Most devices don't require than 2GBps. Also comparing it to the old Mac Pro is kind of depressing -- PCIe 2.0 and only 4 slots is extremely anemic. I think it's probably more reasonable to compare the nMP to other workstations: Sure, it can do 36 devices over TB, but who needs 36 devices? That drives far outside the realm of "common use-cases" and into silliness territory. Moreover, a fairly inexpensive workstation motherboard will often have 7 or 8 PCIe slots with extremely high bandwidth. I guess it comes down to what you really need: 36 little boxes sharing a measly 6GB/s Bandwidth or 8+ PCIe slots sharing between 40GBps - 80GBps (for dual processor motherboards).
The only issue really is price for what you're getting; as you've pointed out there are some grossly over-priced Thunderbolt peripherals right now, using less than premium parts, which is just unacceptable. But without serious competition that isn't likely to change, so I really do hope Thunderbolt will finally start to take off, but that may struggle to happen until Intel realises their tight grip is strangling the market.
The fundamental point when talking about TB as a replacement for PCIe is that TB will always be more expensive and prone to failure, simply due to the fact that you're basically externalizing a PCIe card, which requires separate housing and separate PSU. The marginal cost of adding a slot, some space, and some extra power to a Tower/Mainboard is almost nothing, the marginal cost of adding all those things outside the case is going to be much more.
This is why, I think, TB will never be a replacement for PCIe on desktop PCs/Workstations: It is always going to be less efficient. At best, it'll be a supplement to PCIe (once TB2 goes optical, perhaps loop networks will be good for small businesses) and a useful addition for laptops.
I actually just bought a new MacBook Pro with TB2 and am imagining that someday I might even buy a TB2 product and take advantage of this amazing expandability found in a laptop! By contrast, I have no regrets whatsoever purchasing my PC without thunderbolt as it has 7 PCIe slots. Likewise, if it were even possible to get a TB expansion card for my Mac Pro (it isn't, and likely never will be), I wouldn't take it if they were giving it away.
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