More important than the difference between Thunderbolt, USB, Firewire, and PCIe... choosing the right unit (one known to be rock-solid and provide low round-trip latency) is the important factor.
Make the right choice, and you'll be happy with any of the above.
ie: The best USB audio interfaces offer low round-trip latency right on par with the best PCIe units.
Obviously PCIe and Thunderbolt offer the most bandwidth.
But... if you're not using anywhere close to that bandwidth (which 99% aren't/won't), it's a moot point.
If you drive a car that tops out at 100MPH, it doesn't matter whether you travel a two-lane highway or a twelve-lane highway. The car will only go 100MPH.
Some folks ask why Thunderbolt hasn't taken off in a big way.
Thunderbolt basically provides access to the PCIe bus.
With tower PCs, we've had that for a long while.
Thus, Thunderbolt is most beneficial/significant on small-form-factor machines which otherwise wouldn't provide access to the PCIe bus (laptops and other small machines that wouldn't otherwise provide access to the PCIe bus)..
The second reason is cost. ie: Until the recent rebate, the Apollo's Thunderbolt option was $500.
Most Thunderbolt peripherals are (relatively speaking) expensive. Look at Thunderbolt external HDs vs. USB3.
By comparison, USB is on every machine... and is cheap to manufacture.