Because it will let you have any port you want. I'm sick of apple removing ports as they see fit. Thunderbolt implements PCIe, so you can stick any other port on the end of the cable - USB, FW, eSata.
"Secondly, it may be (theoretically) faster than USB3, but that's irrelevant as hard drives/ SSDs cannot keep up with the speed of either in the first place"
Drive arrays can keep up. Check it out - it's called RAID.