USB 3.0 vs. Thunderbolt is an issue for all pro users of recent Macs and, increasingly, high-end Windows systems. They're both standard on all Macs, so the issue is how much can you rely on the cheaper USB 3.0.
Bottom line: For many Mac users Thunderbolt will be overkill. But if you need workstation performance, USB is no substitute.
Thunderbolt is highly available. In the 18 months I've used my Promise Thunderbolt array, it has gone offline less than half a dozen times--and not at all since I installed Mac OS 10.8 Mountain Lion. Considering the Promise array was purchased shortly after Thunderbolt started shipping, this speaks well for the robustness and maturity of Thunderbolt's underlying Intel technology.
USB 3.0 availability is spotty. Drives drop off for no reason and it takes unplugging and re-plugging or, in serious cases, restarting the system to see them again.
As I use a four-port and a seven-port hub with different chipsets I've found that the four-port--with a newer chip set--is more reliable than the seven-port's older chip set. But I've also found with USB 2.0 that more than four ports are less reliable, which may be the issue with the seven-port USB 3.0 as well.
There are no Thunderbolt hubs; instead, Thunderbolt daisy chains up to six devices together. Overall, the ability to support multiple drives and multiple devices seems to be much more robust on Thunderbolt than on USB 3.0.
USB 3.0 performance is excellent compared to USB 2.0, which was never as good as the ubiquitous 480Mbps metric claimed. It is faster than any single hard drive and fast enough to saturate almost any single SSD as well.
I haven't been able to max out my Thunderbolt connection yet. The four-drive Pegasus array maxed out at something over 400MBps, well within the 1GBps performance of Thunderbolt. However, the ability to plug a second--and third--monitor into the Thunderbolt daisy chain gives a better idea of the total bandwidth.
Even a 10Gbps USB 3.0 will still have less than half of the total cross-sectional bandwidth of today's Thunderbolt. But tomorrow's Thunderbolt is coming soon.
This is why most professionals will choose Thunderbolt in addition to USB 3.0. Need Fibre Channel? SDI? PCIe slots? Genlock? RED workflow? You're the target market.
Don't know what most of those are? You aren't.
USB 3.0--the version most systems will have for the next two to three years--is plenty fast for casual users who need an external drive for capacity or backup. It should work well for direct connection to a small RAID array as well. And, of course, it's compatible with all the USB 2.x peripherals you already own.
But if your livelihood depends on your system and you need external storage, displays, and/or specialized hardware, you'll appreciate the robustness and performance of Thunderbolt. It allows a small notebook--in my case, a MacBook Air--to be a capable desktop replacement.
Will USB 3.0 crush Thunderbolt? It's instructive to consider FireWire's fate.
While the FireWire market was much smaller, it also had a number of specialized products that worked well for professionals, many of which are still available. Thunderbolt replaces FW800 nicely and is well populated with unique products that offer performance that USB 3.0 can't match today.
Yes, Thunderbolt products cost more, but you get more. And if you need more--whatever "more" is--Thunderbolt is the way to go.
Comments welcome, of course. Check out my review of the Thunderbolt Display/MacBook Air combo or more on my experience with Thunderbolt. What say you, fellow Thunderbolt users?