Notes on the past, present, and future of the Mac Pro
It is helpful to think back a bit to differences between the original 2006 Mac Pro and the current version. In 2006 [1,1 and 2,1], there was a single base model which could be customized via build-to-order options for its dual CPUs, graphics cards, and so on. This approach continued with the speed increase in the 2008 [3,1] -- one dual-CPU base model with a limited but intelligent range of BTO options.
In 2009, however, the Mac Pro line was split into two base configurations -- a single-CPU machine and a true dual-CPU Mac Pro. This was an important watershed, away from the original vision for the Mac Pro. The original Mac Pro continued, but a low-end single-CPU server replaced the base configuration. In other words, in 2009 the base configuration for the true dual-CPU Mac Pro jumped from one price point to another -- from $2499 to $3299 [4,1] -- and today it is at $3799 [5,1]. The low-end $2499 base price point was filled by a single-CPU Mac Pro that was basically a server -- a shift that became clear in late 2010 with the final discontinuation of Xserve and the official introduction of the current "Mac Pro Server" (and "Mac mini Server"). Following in the wake of this server-hardware shift was the change in the Mac OS X Server software from a separate product to an add-on in Lion and Mountain Lion.
So today the choice is explicit -- you can buy a low-end single-CPU Mac Pro that is basically a server but has all the internal storage, memory, and expansion capacities of the dual-CPU Mac Pro, or you can buy a true Mac Pro starting at a somewhat higher price point.
In short, the original essence of the Mac Pro is the dual processors. As a result, a Thunderbolt iMac could well replace a Mac Pro for some users, especially those using single-CPU Mac Pro machines now -- but it cannot replace the original meaning of "Pro" in the Mac Pro -- the iMac will never be a multiple-processor machine.
What does this history mean for the future? I think the big questions are:
 Does Tim Cook's Apple see a true Mac Pro (which I've defined here as having more than one CPU) as a machine worth producing? I think the answer here is yes. I don't think he would have responded last year (June) with the "we're working on something really great for later next year" statement if he did not intend to continue the line. [I know nobody here is disputing this point, but I seem to remember a few people doing so in some of the other threads.]
 Will Apple continue to use the Mac Pro and Mac Mini form factors for its servers? I tend to think the answer here is also yes. It took them three years (2009-2011) to make the transition from Xserve/Mac OS X Server to the current approach. Tim Cook was in charge for much of that transition. I don't see them going back.
 Is it possible that the Mac Pro Server will be discontinued, absorbed by increasing speed and capacity in the Mac mini Server? This one is tougher. I think it is a possibility. It's hard for me to see it happening before Haswell, though:
A few more points:
[A] Obviously, Apple pulled the plug on Sandy Bridge EP (E5) processors last year after almost nine months of delays (originally due Q3 2011, they weren't shipped until Q2 2012). Intel is skipping Sandy Bridge EX (E7) altogether and going straight to Ivy Bridge EX (E7). While the latter doesn't affect the dual-CPU Mac Pro, my instinct is that Apple likes to keep its development options open and the Sandy Bridge Xeon bugs that resulted in its highest-end processors being aborted scared Apple away.
[B] I don't think it is at all realistic for Haswell EP (E5) Xeons to appear in time for a 2013 Mac Pro. So we're looking at the Ivy Bridge EP (E5) Xeons, which are next up -- the Ivy Bridge E3s are already out, and the E5s will come before (or together with) the E7s.
[C] In addition, any Ivy Bridge Mac Pro design will transition easily to Haswell, the "tock" to Ivy Bridge's 22 nm "tick" -- so there is no reason to wait for Haswell's engineering advances, like transactional memory:
Those programming benefits will come in a straightforward 2014 refresh of the 2013 design -- think 2014 WWDC.
[I] We'll see a new dual-CPU Ivy Bridge Mac Pro this year starting at about $3299. The base configuration will have a Fusion drive. It will hold up to four 3.5-inch hard drives. The design will also leverage the difference in size between a SSD and a 3.5-inch HDD. You'll be able to put up to eight SSDs in it -- SSD prices in the future may fall to the point where people would be able to do that. I think any new Mac Pro design has to recognize this changing technology.
[II] There may or may not be a low-end single-CPU Mac Pro Server option, as there is today. I think there is still a place for a 3.5-inch-hard-drive server in Apple's lineup, but I don't know how long that will be true -- the continuing development of SSD storage capacity will eventually kill the Mac Pro Server, IMHO. The day you can fit 4 TB of SSD storage into a Mac mini Server will be the end.
[III] Finally, as you might have gathered, while I'd love to see real innovation, I don't think anything truly different (like some of the things dreamed up in these various Mac Pro threads) is going to happen now. That's further off. What we have now is Apple adjusting the Mac Pro to the present and immediate future, not something more distant.
Edited by TenThousandThings - 1/20/13 at 2:12pm