I'd put my money on an entirely new Mac model. It's already known that the Mac Pro is being updated with a smaller form-factor, but there's still a space between it and the iMac that could stand to be filled. Something screen-less, more expandable than the Mini, but less powerful than the Mac Pro.
PCI slots are the new floppy drive: lot of people think they can't live without, they will scream bloody murder when Apple releases a new Mac Peo without PCI slots, but in reality Thunderbolt has just made internal PCI obsolete.
There will not be 3 models. A Mac Pro with PCI slots is just a temporary stop-gap like iPod Classic until all the PCI card vendors have transformed their products into external Thunderbolt devices.
The future will have a small Mac Mini and a big Mac Mini, the latter with the required cpu/ram for server purposes.
> But in reality Thunderbolt has just made internal PCI obsolete.
The current Thunderbolt implementation transfers up to 10 gigabits/second bi-directional. [1]
The current PCI-E X16 slots in the Mac Pro transfer up to 64 gigabits/second bi-directional. The future PCI-E X16 standard (3.0) has 128 gigabits/second bi-directional. [2]
Over the next decade, Thunderbolt transfer rates will reach 100 gigabits/second bi-directional. [3]
Thunderbolt is nowhere close to replacing PCI-E slots within computers.
Sadly, I don't think we'll ever see a matte screen iMac ever. The iMac is geared towards the consumer market, and the general consumer market prefers glossy screens.