PCIe 3.0+ PCB requirement
Bog standard FR4, the type used as standard by PCB manufacturers is not really up to the task of Gen3 PCIe. 

The weave is much too coarse which means that as the pair runs along the board, the impedance changes continuously due to the dielectric constant varying. The image below tells a thousand words. Standard FR4 is on the left.


Image Source

In order to avoid degrading the signal so much, for high speeds like this we tend to use a higher quality substrate. This can range from higher quality FR4 all the way to very expensive exotic ceramic materials like Rogers.

We've had reasonable success over short distances (~10cm or so) using a comparatively low cost "High-Tg FR-4" material - this is basically still fibreglass, but the weave is much more tightly packed, as shown in the right hand diagram of the picture, which means the dielectric constant doesn't vary as much. In particular we use VENTEC VT-47, though there are many high-Tg materials out there, it will depend on what your fab house has available.

For longer distance traces or going through multiple connections such as backplanes, you will have to experiment or model to see if your drivers can cope. In this case you could go for a more expensive Rogers substrate. Alternatively an option we've used in the past is to add a PCIe Redriver IC (such as DS80PCI402), which will allow you to tune the drive strength of your differential pairs to compensate for some of the effects of impedance mismatch.