Steve,
PCIe is the standard protocol for high-speed serial computer expansion bus design, which is developed and maintained by lots of companies and groups. It is different from HyperLink, which is the protocol developed by TI for high-speed communication between KeyStone devices.
I agree that the learning curve of PCIe protocol might be a littler longer than HyperLink. PCIe could be suitable if we have multiple PCIe Endpoint devices to be connected by switch and controlled by PC host or PCIe Root Complex device. It can also be used for point-to-point communication. But for the point-to-point communication between KeyStone devices, free feel to use HyperLink, which could provide high speed, low pin count and might be easier for the usage.