Hmm,
I am not sure how relevant this is to the topic but let me address a few things from your post.
1) Thunderbolt is much more than a high speed connection for hard drives and storage devices. The reasons behind your university adopting it solely for this reason, if that's the case, are certainly suspicious. But using thunderbolt purely for conventional storage tasks is its least useful function. It gets more useful if you are attaching large fast RAID arrays, but the main purpose of thunderbolt is not the same as USB or even firewire before it. Its is to extend the PCI bus outside the case. USB 3.0 or eventual 3.1 will not likely ever be suitable for these kinds of tasks. TB needs to get faster to make this idea truly flourish but even as is it is a great way to expand on a system that lacks PCI slots. If the devices your Uni is buying are big and clumsy and slow and expensive then they are not making intelligent purchasing decisions. That has little to do with TB itself.
2) Thunderbolt is relatively expensive. It will remain so despite the moaning of so many people. It is not a mainstream tech. It is a technology for people who need a faster professional grade connection and even more so, for those who need PCI bus extension. Intel has made it clear that it intends to integrate TB into the CPU at some future point. When that happens it will by default become more ubiquitous and may drop substantially in price. But it will never be price competitive with USB. They are not the same thing. Again if you are buying single TB drives and paying a boatload for them then in all likelihood (though with some exceptions) you don't understand the purpose of thunderbolt and you are wasting money. Yes apple used to charge $50 for a cable, now they charge $40, and if you ask me your pretty foolish to pay even that much since you can easily find cables for sale online in the $20-30 range (sometimes even cheaper). The cable has active chips in it, it will never be a cheap cable. It will get cheaper, but it will probably never be cheap. Get over it. At some point we will see fiber based cables as intel had originally intended.
3) While USB 3.1 will be a nice addition to the connectivity landscape, it is still not TB, they are different things with different purposes. USB 3.1 wont fundamentally change anything. It will continue to be good for the things USB 3.0 is good for. TB will continue to lead in overall speed and in the extended functions of carrying PCI and displayport signals. Thunderbolt is not going away. Intel makes the chips we all use and intel is putting thunderbolt on those chips eventually. Intel may take a very long time to support USB 3.1 natively, though again, doing so has nothing to do with TB replacement.
4) Thunderbolt is very important to OS X users, whether we like it or not. As of the release of the new mac pro, there will be exactly zero apple computers with PCI slots. This will have a very strong affect on the types of peripherals and driver support that is available in OS X going forward. There will be many legacy PCIe devices that never receive proper future OS X driver updates and there will be many new PCIe devices that never have drivers written for OS X. Because of Apple's decision, you can hate it or love it, TB will become synonymous with OS X. If you want to use OS X, you need to be taking TB very seriously now. That choice has been made for you.
5) Firewire was not a failure, it was extremely popular in certain fields such as media. That 95% percent of the PC universe ignored it i couldn't care less. It was a decent premium technology for the time. Firewire had some advantages over USB but they were fairly direct competitors. TB is not a competitor to USB. Its is a very different technology. I guess i am just sick and tired of hearing people compare USB and thunderbolt. At best it reveals a complete lack of understanding of what TB is and what types of usage it is mainly intended for.
g\
[EDIT]
Now on some very relevant news....
GA-Z87X-UD5 TH is available for purchase today
AND!!!!
GA-Z87X-UD7 TH is confirmed to be TB2.
So cool. Still wonder how much its going to cost us but that definitely makes it the hack board to own when it launches:
http://www.youtube.com/watch?v=YwTi_WY_Eco