Comparing thunderbolt and USB 3.0 is like apples and oranges. They are quite different in how they work. Thunderbolt effectively extends the PCI bus over cables (and now there are Thunderbolt fiber optic cables that can go hundreds of feet), so you can put anything on the end of the cable you can plug into a PCI slot. So far products using thunderbolt are more expensive, but they are way more flexible, especially for adding complex devices to laptops or mini's. I am actually surprised no PC vendors have not added it already since it is an Intel SPEC not Apple.
USB 3.0 on the other hand is just faster USB. Very flexible and great for high speed peripherals like external hard drives, cameras etc. The device driver model is completely different to Thunderbolt though.
The primary reason for a faster USB 3.0 spec is really for external data storage as the latest SSD drives (especially in RAID) can swamp out even the current USB 3.0 spec. And by the time super speed USB 3.0 arrives, the drives will likely be much faster and will need 10G connections to keep up.
At the end of the day they really serve different purposes, which is the reason the latest Mac's come with both. I doubt it will ever be one or the other.