This means you can run a PCIE 3.0 4x+ lane NVMe SSD like the Intel 750 while also running a 3.0 16x GPU (or two GPUs in SLI/CrossFireX). Given an appropriate board, anyway - I haven't looked at Skylake boards.
The performance increase of PCIE NVMe SSDs over SATA SSDs is amazing. SSDs are already great of course, but the Intel 750 can decrease load times by another order of magnitude.
Looking at the linked motherboard, its PCIE 3.0 slots are shared bandwidth, which isn't taking advantage of Skylake at all.
Edit: Actually, looking at the launch boards in Anandtech's review, most of them are routing the extra PCIE 3.0 lanes to M.2 ports (potentially a step backwards from U.2 but forwards from SATA). Getting maximum performance out of a NVMe SSD is seemingly still going to be restricted to only certain high-end boards for the time being.
At a glance, it looks like the "MSI Z170A Gaming M9 ACK" board has a dedicated 3.0 x4 slot separate and supports U.2, so there's at least some available, but it's $400.
Edit2: Apparently Skylake M.2 slots can provide full 3.0 x4 performance, so they're probably fine.