It seems external harddrives still have the edge over thumb drives in storage capacity. There aren't USB thumb drives that can store terabytes of stuff -- it seems like the biggest they make is 1 TB. I'm confused by the pricing since 1 TB USB 2 is really affordable ($20-30), but 1 TB USB 3 is like $600.
USB3 is backwards compatible to USB2, but that's really the only commonality. It's a leap of several generations beyond USB2. USB3 has about 10 times the data transfer rate. Also, it's a true duplex (can send AND receive simultaneously), while USB2 is more of a simplex (can send OR receive). If you're moving large chunks of data around, like during a backup, the extra speed of the USB3 interface makes it that much more valuable, hence the $$$ price tag.
Also, while I am not an electronics engineer, I suspect that the flash memory in the USB3 thumb drives has to be faster then the USB2 drives to take advantage of the higher speed data.