I think Apple has really dropped the ball with the new Mac Pro - it is like the Cube, it looks cool but the Mac Pro is not a machine that requires form over function - people buy them to upgrade them, swap things in and out, stick them in racks, etc. Thunderbolt is not a replacement for pro use expandability - it just means a lot more cost + a lot more (very expensive) cables + a performance hit.
A good excuse for Apple to discontinue the Pro line eventually though - "hey we made this great new machine, but nobody bought it, so sorry"
Guy English made some great points about potential for the new Mac Pro:
"The CPU is a front end to a couple of very capable massively parallel processors at the end of a relatively fast bus. One of those GPUs isn’t even hooked up to do graphics. I think that’s a serious tell. If you leverage your massively parallel GPU to run a computation that runs even one second and in that time you can’t update your screen, that’s a problem. Have one GPU dedicated to rendering and a second available for serious computation and you’ve got an architecture that’ll feel incredible to work with."
Right now it's trendy to criticize the new Mac Pro for boxes it doesn't check that the current version does; mainly a lack of enclosure space. That's something Apple can easily address with their in store setups. But when the thing releases all anyone will be able to talk about is how much Apple is charging for the high end version with the E5 2697 and 2 W9000 Firepro cards.
I think what he meant was that the current benchmarks are unable to quantify the benefit to users of having a GPU for computational power while the other is driving the displays. The new Pro configuration suggests you'll be working in real-time when doing graphically intensive tasks rather than waiting for something to render. Animators & video editors will benefit from this in ways that are difficult to slap a technical benchmark on.
These machines are probably aiming to scoop up some high-margin high-end workstation business, hence the demo by Pixar at the last WWDC.
I'd like for Apple to carry both lines going forward, but I guess that is unlikely. The issues I'm seeing now discourage me from dropping another 3-5k on the new ones knowing they are even further from being fixable.
The new Mac Pro 2013 is beautiful man. I'm not the target market, but I can see professional audio/video engineers getting excited about it. Editing 4K video in real time? Pretty badass. I was also impressed with the case engineering, but we'll have to see how it performs. I don't really see the design as form over function. It was designed to use a single fan for the entire machine.
I think that the jury is still out on if there will be a significant performance hit. Thunderbolt is like having a direct connection to the PCIe bus, isn't it? Now, you're right about the extra cost, but I think that they will still be sufficiently upgradeable, albeit with more cost and fewer choices.