For most users, USB 3.1 will cover nearly all needs. A regular hard drive connected via USB 3.1 will run just as fast as with Thunderbolt. In fact, a single SSD will not run any faster with Thunderbolt. USB 3.1 gives the goodness of TB1 plus some backwards compatibility. While TB2 remains faster, for the typical user, it has little value when cost is considered.
With more dynamic set ups, TB come into its own with with TB2 and RAIDS that offer improved speed (RAID 0 etc.). Also, with some "smartware," TB can do more clever communication tricks as USB has one upstream and one downstream while TB has 2 up and 2 down which can be as needed, arbitrated or allocated. While the latter isn't really in play, it is possible. In the meanwhile, I hope to see USB 3.1 with its subset USB-c take the lead on being cheaper than the disgraceful Apple introduction of TB without any real devices to attach. Why introduce something with no devices? At least pay a 3rd party or provide it yourself, Apple. (bicker bicker)