In what way would Thunderbolt be better, apart from the somewhat higher bandwidth (10 Gbps for Thunderbolt vs 5 Gbps for USB3)?
ThunderBolt is actually 40gbs (2 channels at 20gbs each). Also, that's the data rate, not the signaling rate as it is with USB. USB's data rate is less than a third of it's signalling rate. That's why you only get 15Mbs out of a 480mbs USB 2 connection.
Thunderbolt is also DMA driven, not CPU driven. Therefore it's speed isn't affected by what you are doing on the computer. Ever tried transferring video over USB? Get dropouts while you computer was busy? That's why data transfers should be DMA driven.
ThunderBolt also runs the PCIe protocol, it's basically a PCIe extender melded with Display Port. Give you any ideas? How about an external video card that you can move between machines? Or an external SSD that's actually faster than an internal drive? (although they would probably use a SATA drive in the external case).
Also, ThunderBolt provides 10w of power to attached devices. That's enough to run a desktop hard drive, or the SSD mentioned above.
And finally, because it supports video - it uses a MDP connector - you have one cable to rule them all. Your display and all your peripherals use the same cable - they even daisy chain. Not the mish-mash of 30 different connector types we have to deal with now (USB A, USB B, Mini, Micro, HDMI, DP, MDP, DVI-I, DVI-D, etc, etc, etc.)
It's downside is that being an active connection it's expensive. Cables are $20 instead of $3. Although the nice thing about active cables is it's much more difficult to end up with a crappy junk cable. It probably costs MB makers an additional $20 to add it to their boards.
Unfortunately the $20 extra is what's going to make ThunderBolt fail. How often do you see people in these forums asking what's the cheapest motherboard, or cheapest CPU. They rarely ask what's a GOOD motherboard. Welcome to the race to the bottom.