Intel's decision will not only better unify available ports on newer hardware, but will offer identical power and data transfers than current USB-C cables. While in Thunderbolt mode, this is when Intel really steams ahead of competitors by offering a higher throughput of 40Gbps, double that what is available through Thunderbolt 2.
This could cause confusion for some who may be expecting said improved transfer speeds, but are unable to due to hardware not supporting Thunderbolt 3. Intel notes that current Thunderbolt (and Thunderbolt 2) peripherals will support the new format with an adapter. It's a solid victory for those who are fighting for a unified interface between computers and other hardware.
Intel expects the first wave of Thunderbolt 3 products to ship by the end of this year.