The third version of Thunderbolt now has USB protocol included. Well, in a way it is. The real and technical way to see this is: the new Type-C connector is adopted by USB-C / USB 3.1 and Thunderbolt 3. In other word, Thunderbolt 3 is not compatible with Thunderbolt 2/1. (Oh..yeah... who does not like all the new convertors and adapters? some vendors sis going to make some money.., and you as a loyal Thunderbolt users must pay extra fee for the converters, in result, you will have all the different convertors and adapters all over the places, Thank you TECHNOLOGY !)
So do you really need Thunderbolt1/2? well, depends. If you want something really fast, Thunderbolt 1 and 2 are capable to give you speed up to 1GMB/sec, to be more specifically, it's 1375MB/sec, on the data transfer. Take LaCie or CalDigit's RAID as an example, with Thunderbolt 2 computers, you can reach 1375MB/s from their RAID unit. Is that cool? well, of course, big time saver.
The following Thunderbolt storages are capable to let you reach that magic 1375MB/s, if you use SSDs in them. The HDDs would be slower but fast enough for you to do anything you want.
OWC ThunderBay 4 0GB 4-Bay Professional Grade Enclosure w/ Thunderbolt 2
LaCie Little Big Disk Thunderbolt-2 Portable Hard Drive 1TB SSD (9000477)
CalDigit T4 Thunderbolt 2 Professional RAID 0, 1, 5, JBOD External Hard Drive (T4R-20000-US-150)
Do you need Thunderbolt 3 device? the answer is, YES and NO. Why? because remember, Thunderbolt 3 now can do USB. Who has bigger domain? USB of course, at least in the next 5 years. That being said, even if you have Thunderbolt 3 computers, you will be able to use any kind of USB devices that you have been using for the past 20 years. Plug & play as Intel has promised.
The good thing about Thunderbolt 3 is that more and more PC desktops and laptops are forced to adopt to Thunderbolt 3 as Skylake from Intel has Thunderbolt 3 builtin. Free of charge. Thus, you will probably buy a Thunderbolt 3 computer or laptop without knowing you have the latest and perhaps the fastest external interface in the world.
So how fast is Thunderbolt 3? Intel says, double of thunderbolt 2. What does that mean to you? well, it would probably mean nothing to you as you do not really care about Thunderbolt 3, but USB 3.1 10G. However, if you are willing to dive in to a faster domain, bite the bullet and buy an expansive Thunderbolt device, you will see the big difference especially on the SSD or Docking station.
Remember, Thunderbolt is PCIe hence being an external PCIe dock v.s. USB dock is huge different. PCIe in Thunderbolt 1/2/3 has 4x lanes, each lane can talk to a dedicated controller, for example, USB, or Ethernet or SATA. The USB dock on the other hand can only do the conversion job from USB to SATA, USB to Ethernet, or USB hubs. That would definitely slower down the performance, no dedication channel.
So if you want a real good Docking station, perhaps Thunderbolt is way better than USB.
Another cool improved thing from Thunderbolt 2, is the Power. Thunderbolt 3 can do power delivery and can charge your laptop or device at 15W. Thanks to Type-C connector. This same power delivery also applies to USB-C, so it's not unique to Thunderbolt 3.
Likewise, Thunderbolt 3 can also do Display where it is identical to USB-C since both are using Type-C connector.
Thus, aside the 40GB/sec bandwidth (Data and Video), Thunderbolt has same DisplayPort and Power Delivery functions that USB-C has. And of course, Thunderbolt 3 can do higher bandwidth and data rate on the transfer, that means you may have dual 4K monitor output from it where the current USB-C Gen1 5G or 10G can only do 1x 4K.
Bottom line is, it's your call to choose either Thunderbolt 3 or USB-C, just to make sure the cable selection would not kill you right there as the cable would be huge messy in the future. Label them correctly and nicely to prevent confusion. I would think of the easiest way.... only buy Thunderbolt 3 cables, but use it along with USB-C devices. LOL.