Choosing USB3 is not unreasonable. No computer I currently have access to currently has a Thunderbolt port. On the other hand, every computer I have access to has at least USB 2.0. Since USB is forward-compatible, I could connect a USB3 drive to one of these computers and get access to my data. On the other hand, if I had a single Thunderbolt computer and put my data on a Thunderbolt drive, it would be quite inconvenient to get access to my data if something went wrong with that computer. You like Thunderbolt, that's clear, and it's a good choice for you. But it's not the only sensible choice for everyone, and I hope the next iMac provides choice in the matter.
I have a couple of 1.5TB Seagate GoFlex drives that I bought at Costco. These drives come with a USB 3.0 interface... but the interface is replaceable. One option is a Thunderbolt adapter. This allows different interfaces with different computers.
Currently none of my computers have a USB 3.0 interface. Hopefully that will change once I upgrade to the '12 iMac. Like you, all of my computers have USB 2.0... but I also have a single machine (MacBook Air) with TB.
As an experiment, I bought the Seagate Thunderbolt adapter. I ran some tests to compare the difference between USB 2.0 and Thunderbolt. I created a 25GB folder of large files (69 files)... and then timed read/write speeds with USB 2.0, and then with TB. Time below is measured in minutes to transfer 25GB using the Seagate 1.5TB GoFlex hard drive.
HDD on USB 2.0: 11:44 (read) - 14:52(write)
HDD on Thunderbolt: 5:05 (read) - 4:36 (write)
Then I ran the same test using the same TB adapter with an older SSD that I had hanging around:
SSD on Thunderbolt: 1:43 (read) - 3:55 (write)
By comparing the HDD vs SSD performance on TB, one conclusion that I reached is that the HDD TB performance appears to limited by the disk drive, not by TB. Whether the HDD would be equally fast on USB 3.0 (vs TB) is unknown... but I suspect that a single cheap USB 3.0 HDD would probably be close to the same speed as it is on TB because HDDs are slow. I would not expect the same with a single SSD... and I will test that once I finally have a USB 3.0 machine. I suspect (but have not proved) that a good SSD will always be faster on TB vs USB 3.0.
I certainly agree with those who feel that direct attached RAID boxes will benefit from Thunderbolt. They are fast, expensive, and are used on workloads where users are willing to pay for performance.
Currently... if was purchasing external storage, I would go with the following:
External HDD: USB 3.0 (because of cost)
External SSD: Thunderbolt (because of performance)
Direct attached RAID: Thunderbolt (because of performance)
/Jim