Well, historically with USB vs Thunderbolt, USB uses more CPU. In the case of USB 3.0 vs Thunderbolt, that difference has been minimized. I guess, arguably, the FirmTek USB 3.0 enclosure peaks at ~50% more CPU usage than Thunderbolt, which is not a good thing.
Also, up till now USB 3.0 has not given the performance of some of the good Thunderbolt enclosures. The FirmTek apparently solves that issue.
So what it comes down to is not whether you'd pick one over the other, but making sure you pick the right subset of one over the other. You can't just go buy any old USB 3.0 enclosure and see numbers like in this thread, in the same way you can't do that with Thunderbolt either.
So it's really a choice between a Seagate Backup Plus/Buffalo MiniStation + Thunderbolt SSD or FirmTek USB 3.0 + SSD. Up to you, really.
I don't have the FirmTek to test, or I'd be able to give more constructive advice.