They really could have used a few PCI slots for things like 10GB or 40GB ethernet, and whatever comes down the pike. I wish they still kept the “big box” format around in conjunction with the new “tube” design....
My limited understanding is that Thunderbolt is basically a transport layer for PCI Express, and TB2 should have enough overhead to be just as fast, even with multiple cards. I bet there are engineers at Belkin and Griffin already working on an expansion chassis full of drive bays and PCI slots that looks a lot like the old Mac Pro box; maybe even with room to put the black cylinder inside it.