Really there is no decent reason that anyone can point to as to why they didn't do SOMETHING.
Occam's Razor, the simplest hypothesis is the most likely the best fit. If Apple wasn't working on anything they wouldn't produce anything new.
So, if at one point they didn't want to continue the product, then there were no updates while that decision held.
It is not a strategic product. It is not the primary Mac. It isn't even the primary desktop Mac. With the tweaks to the MBA it is now the worst selling Mac product line and lowest growth of any Mac in their Mac line up.
It is very decent reason. It is just one that folks refuse to accept in this forum. For the better, there appears to have been a change of mind and they now want to give it another shot.
They didn't need to redesign the case,
Actually the do need to redesign the case. The case's basic design constraints revolve around the state of technology about 7-8 years ago. The XServe is gone so the gratuitously bad horizontal racking makes a larger difference now. ODDs are on their way out along with dual 5.25" bays. RAID-0 isn't as necessary as it was with advent of SSDs. Max RPM drives are now just as likely to be 2.5" drives. Higer end GPU card run almost twice as hot as they used to and are at least a dominant, if not more so, thermal problem inside of a workstation. High performance Wifi means MIMO (multiple antennas ) now.
The case is out synch with modern components with the except of the CPU packages. Does it need to be radically different? No. But very material updates are needed to remain competitive.
and they could've integrated Thunderbolt on the logic board in the same way that PC motherboards are starting to do,
Thunderbolt is probably the least motivated change they could make to a new Mac Pro. It solves a problem that Mac Pro's don't have ( multple video out already present on GPU card backplanes and PCI-e expansion represented by the Mac Pro's 4 slots. )
The competitive workstations upgrades have focused far more on SATAIII flexibility, built in RAID capabilities , and USB 3.0 rather than Thunderbolt. Also, hosting high end dual GPGPU card set-ups is far more common.
No workstation has Thunderbolt. Their is no huge industry rush in that direction. If Apple left Thunderbolt off the 2013 Mac Pro, but added leading edge GPGPUs , USB 3.0 , and substantive computational speed increase, the core Mac Pro market would still buy it.
while leaving the video card to have DVI and HDMI while still feeding the video card's signal through the Thunderbolt port.
There is about zero need to feed the standard form factor PCI-e GPU card's output video through Thunderbolt. It really doesn't buy much. The GPU card's connectors hook to monitors just as well as in most standard contexts as Thunderbolt cables do. In fact better when it comes to DisplayPort 1.2, since Thunderbolt is only 1.1a. The marginal significant benefit of Thunderbolt might be running signal over optical connections over longer distances. Optical Thunderbolt, although promised for late 2012, still really hasn't arrived. Most workstation deployments are not trying to but the system unit as far away as possible from the display. ( Yeah there are corner cases, but those folks aren't the mainstream workstation market. )
The 27" iMacs have separate boards.
Given the recent teardowns of the 2012 21.5" iMacs that is more likely iMacs used to have separate boards. Apple may be still using cards for the 27" model, but it looks like they are starting to apply the same "soldered to the motherboard" approach they use on the new MBP updates to the iMac also.
The mobile "unofficial standard" boards aren't really representative examples in the workstation space. But yes it wouldn't be hard to embed a GPU into a Mac Pro.
Plus Thunderbolt-equipped motherboards exist and they pipe out the discrete video card's signal. Presumably, this is what would happen with a Thunderbolt Mac Pro.
Not likely. "Loop back cables' are not a solution that Apple would adopt. Most of the PC industry isn't going to either. There is nothing wrong with having multiple video cables going to multiple monitors.
It was never stated when in 2013 the next Mac Pro would arrive. They could release one in November and it'd technically be on time.
Above you are lamenting the Apple should have dropped an upgrade in 2012 and now "late as possible will be OK". It can't be both.
"On time" is not material to health of Mac Pro market. If Apple waits more than 12 months to "fix" the tepid, limited June 2012 upgrade then they are going to loose customers. The longer they wait the more will leave.
The 2006/2007 Mac Pros are going on the Vintage list soon. Many of the 2008 models are going to be outclassed by a Mac Mini pretty soon too when they go Haswell. Ivy Bridge Xeon E5s are not going to "buy back" folks who bought something else already. A Sandy Bridge Mac Pro would outclass most equivalently priced 2009 and prior model.