I can't imagine scenario where PCIe 3.0 is not enough for me. Even for storage it only matters for a linear I/O and I don't care about it that much. Random I/O won't saturate PCIe interface, it's not fast enough on any disk.
It might not be useful now but in terms of future proofing a system it might become more of a deciding factor. The ability to make use of drives, graphics cards, network interfaces, or anything that can connect via PCIe for a few years to come might be beneficial.
