So I guess the official branding of Lightpeak is Thunderbolt, even from Intel? And the standard connector (even outside of Apple products) is essentially Mini-Displayport?
Of course, it kind of messes with the third-party accessory market, but I'm sure they'd love another reason to get people to buy new stuff.
The big issue with replacing any iOS connectors with desktop standard connectors is power. Thunderbolt specifies 10W of power; USB specifies 2.5W; the Camera Connection Kit only supplies 0.5W. I doubt that Apple is going to ship anything that provides much more power than that.
So if anything prevents usage of PCIe in embedded devices it's added complexity, not power requirements. By the way electrical interface of most modern true-color TFT panels is identical on the lowest layer to PCIe (and SATA and who knows what else).