That's incorrect, I'm on a skylake NUC which definitely has PCIe 3.0 x4
I'm assuming you have a 950 pro 256G. Note that the 512G version has better performance.
My NUC6i3SYK is showing similar results on Ubuntu 15.10 amd64 with 950 pro 256G: 1120MB/sec read
The 950 pro is indeed connected via PCIe 3.0 x4. You can confirm that by running "sudo lspci -vv", which shows 8GT/s x4. I think that is normal behavior. You might perform a write benchmark, which will give you the result ~900MB/sec, identical to the specification.