For me the issue isn't two GPUs, but the fact that you can't have a x16 slot at full bandwidth, unless you run everything else through the DMI link. Which, as we all know, is a simple PCIe 3.0 x4 interface, with a few bells-and-whistles. This will become a serious limitation in a few years as 10Gbit USB3.1, PCIe storage, 2.5/5/10Gbit Ethernet and perhaps TB3 takes off. Heck, TB3 is capable of fully saturating the DMI link already (40Gbit/s vs 32Gbit/s available).
What Intel should do is simply make a second PCIe x4 link available from the CPU exclusively for PCIe storage. So you'd have a x16/x4/x4(DMI) configuration instead of the current x16/x4(DMI). In other words, keep the PCH to handle all the legacy interfaces, but give the option of a high-speed interface from the CPU.
Hence, my next upgrade will not be desktop Skylake/Kaby Lake/Cannon Lake, but Skylake-E. Consumer or Xeon will depend on what models Intel launches.