This; Thunderbolt 1 basically has two channels, one for general data and one for Displayport, all Thunderbolt 2 does in terms of the cable is turn these both into a single data stream, assuming the various devices are compatible of course, thus doubling the possible speed for all devices involved.
It means things are now a little more complex if you want to hook a display since it's directly sharing bandwidth with other devices, but for things other than the display it's a big bonus. Plus, with six ports on the new Mac Pro, it's not like you're struggling to find places to connect everything; you just need to bear in mind that devices hooked up with a display somewhere in the chain will be sharing closer to Thunderbolt 1's bandwidth, so you don't want anything too demanding in there.