As Marco Arment mentioned numerous times on his blog, and reiterated with his co-hosts on Accidental Tech Podcast, the current generation of Thunderbolt, both in terms of bandwidth and latency, is insufficient to use to augment a laptop with a high-end GPU and pools of CPU and RAM, especially in a daisy-chain scenario. If you attempted such a thing, where you connected, say, an 11" Macbook Air to an external box with a CPU, GPU, and huge pool of RAM, the communication between the laptop's CPU and the resources on the Mac Pro Replacement (henceforth, "MPR") would be way too slow to yield a smooth experience for games, high-end 3d, video editing, etc.
But what about turning the whole formula around. The MPR could be a box with a pair of Xeon CPU's, a really beefy professional GPU, and gobs of RAM, optional hard drive, but no OS. It connects to a Macbook of some sort over Thunderbolt. The laptop suspends the OS, migrates the OS to running on the MPR, and then the MPR takes over, using the laptop as an external display, keyboard, and trackpad, and hard drive.
In other words, most people are thinking of the MPR as a docking station with some additional compute resources, whilst my proposal would make the MPR a fully functional computer sans OS, with the OS and primary storage provided by the externally attached laptop.
Now, I'm not saying Apple will do this, but this is a way they can.