Seems like there are a few different, not-necessarily overlapping use cases for Mac Pros.
There's the people who need lots of CPU.
There's the people who need lots of RAM.
There's people who want lots of fast disk.
There's people who need to use specialized cards.
Trying to serve all at the same time dictates the shape of the machine. (For example, reduce space for cards, and you can make a 1U rack mount.)
Thunderbolt opens up the possibility of replacing the Mac Pro with something akin to a beefed up iMac or maybe a stretched shoebox-shape Mac Mini, with high-end CPUs, lots of RAM slots, and basic graphics and disk, with external Thunderbolt chassis available for disks or expansion cards.
If the main unit + disk chassis + card chassis cost the same as a similar Mac Pro, this would be a significant savings for those customers who only need the main unit and zero or one external chassis.
Unfortunately this is like a high end Commodore64: it starts simple but soon you have a rats nest of cables separate power for all the external devices. I want less cables not more. Also, I don't think thunderbolt cables can be screwed in, so you run the risk that a cable could get tugged and pulled out.
I'm thinking like an 8-drive chassis, and maybe 3- and 6- slot card cages, rather than lots of single-purpose external devices.
Rats nestery need not be too bad. Thunderbolt from the Mac to the drive chassis, then thunderbolt daisy-chained to the PCI card cage chassis. Power cords for the drive chassis and the PCI card cage chassis, if they can't be powered by thunderbolt. (Naturally, how ratty the PCI card cage gets would mostly be determined by what cards it contains and what are plugged into it.)
Not sure what the cable length limits are, but it might be possible to spread these out a fair distance, especially once optical-based Thunderbolt happens. Being able to put the PCI cards close to what they're connecting to, with just a single Thunderbolt cable running back to the computer, could be a cable management win, versus snaking multiple cables to a computer.
I'm sure someone could come up with a screw-in variant of Thunderbolt, but even so, I don't think Mac Pros have any screw-in connectors as it is, apart from the video cables screwing into the video card(s).
There's the people who need lots of CPU. There's the people who need lots of RAM. There's people who want lots of fast disk. There's people who need to use specialized cards.
Trying to serve all at the same time dictates the shape of the machine. (For example, reduce space for cards, and you can make a 1U rack mount.)
Thunderbolt opens up the possibility of replacing the Mac Pro with something akin to a beefed up iMac or maybe a stretched shoebox-shape Mac Mini, with high-end CPUs, lots of RAM slots, and basic graphics and disk, with external Thunderbolt chassis available for disks or expansion cards.
If the main unit + disk chassis + card chassis cost the same as a similar Mac Pro, this would be a significant savings for those customers who only need the main unit and zero or one external chassis.