Considering that USB3.1 (10MBit/sec) is faster than a single PCI-E lane, I would go for a motherboard with USB3.1 integrated, like one of the newer Z170 boards from Gigabyte.
For most people, I don't think it's worth upgrading on purpose.
Aren't there two types of USB 3.1 out?
Well, sorta, but its all in the naming
USB 3.1 Gen 1 (5Gb/sec, or old standard usb 3.0 speeds)
USB 3.1 Gen 1 (10Gb/sec speed, the new usb 3.1 speeds)
I bought a motherboard in 2010 and i picked one with two USB 3.0 ports. At the time there were no USB 3.0 devices. But 3 years later there was many external hard drives with 3.0 and I am so glad I bought that motherboard. I'm still using it to this day. if you want it, get it.
Now there is virtually nothing in the consumer space that saturates USB 3.0 outside of niche hardware.
A simple external SSD is quite capable of that. The most I've ever been able to get out of a USB3 connection (with UASP) is ~430MB/s. This was on a drive that happily does 560MB/s on native SATA3.
Its not USB 3.1 what you want, its USB Type-C. USB 3.1 is merely twice the bandwidth of USB 3.0, USB Type-C is the new connector.
If you're not rushing to buy now, I would wait for Skylake Motherboards with integrated Alpine Ridge controller so you can use either USB Type-C or Thunderbolt 3.