I suspect that the current form factor is going to end.
Change from the general form factor ( rectangular box with removable side, PCI-e slots, and drive slots ) is not likely. Change from approximately the same dimensions and "holes"/sockets on the box; yes.
For example, consider slicing off the 5.25" optical bays
That is pretty tough to do if want to keep a symmetrical design since the power supply is the largest principal member of that top thermal zone. Even if you remove the ODDs, it is still there.
Apple could re-purpose the 5.25" bays. Users somewhat commonly already do that for 2.5" and 3.5" drives. If the Mac Pro mutated to just simply afford what some folks are already doing that would be simply adapting to the market. The Mac Pro needs more 2.5" bays than it has now. It keep it locked just on four 3.5" bays is to keep the design firmly rooted in the past; not the future.
and also two of the PCI card slots - - that would do quite a bit to cut down the size of the box.
Why nuke two PCI-e card slots? It really going to save all that much space if leave two very power hungry x16 PCI-e slots behind.
First, The fan(s) required to cool those are going to soak up about as much space as the fan to cool the 4 slots if go with large diameter , low noise options.
Second, if punting x4 slots for Thunderbolt the likely defacto addition of a embedded GPU ( GPU , VRAM , etc. ) likely consumes just as much space (if not more ) as the two PCI-e slots took.
Third, current Mac Pro splits x4 PCI-e v2.0 bandwidth between the two x4 PCI-e slots with a switch. The vast majority of mainstream PC designs use switches to split x16 bandwidth into two x16 physical but x8 electrical slots as part of the basic board design.
Ditto for cutting out two PCI slots .. and Apple's argument is that they get replaced with Thunderbolt ports - - probably only two (2) total,
since one x4 Thunderbolt controller corresponds to one x4 PCI-e slot it is unlikely that Apple woud claim that two slots was equal to two TB ports. Those two ports only represent one slot.
even though its IMO likely that the FW800 ports will be cut too,
FW800 is probably on a slippery slope but so are the audio sockets. The number of FW800 sockets may go down but still may be above zero. If adding Thunderbolt and attaching it to the PCH's x8 PCI-e v2.0 limited bandwidth then the x1 PCI-e link for FW800 would probably get swapped for a x1 PCI-e link for USB 3.0 unless some other x1 link got squeezed off.
Even if they did for the hard core "can only buy Apple branded stuff" folks would buy the Thunderbolt Display/Docking Station that Apple sells. It puts just as many, if not more, ports back on the combined system as Apple would take away.
A one-for-one correlation between TB and the Ethernet/Firewire/USB sockets is just deeply flawed. The whole "one socket to rule them all" was just marketing kool-aid that Intel (and some others) initially floated to get traction. TB is not the universal socket replacement. It never has been outside of the kool-aid spin-meisters zone.
which means that they really should be four (4) Thunderbolt ports to be "equivalent" to such a loss of both PCI + FW800.
Four TB ports requires two TB controllers. One that is a huge waste of x8 PCI-e lanes. Second, it complicates and limits the display flexibility for the both controllers ( likely at least one of the controllers would be limited to just one Display Port input ).
Next, get rid of using one of the 3.5" bays for the boot drive. Replace it with one of the laptops' SSD solutions and put it on the motherboard.
The 3.5" bays could be moved into the 5.25" bays. Or a subset of the 3.5" bays could be moved one of those (e.g., 1-2 into bay 1 ) and the other bay used for 2.5" drives (e.g. 4 into bay 2 ).
I would suspect at least two if not all four 3.5" bays get moved out of the PCI-e card thermal zone. If Apple is adding an embedded GPU and higher TDP cooling for PCI-e cards into that zone those devices should be moved out to help balance the increase.
This also provides the opportunity for Apple to shrink even further by removing the entire row of the four 3.5" bays under the rationale that storage expansions belong in a Promise R4 Thunderbolt cabinet.
Low to medium workstation storage requirements can be done with 2.5" drives which require less space. There is zero need to appeal to external Thunderbolt boxes.
However, for very large data storage that
is where folks go already.
At this point, we should look to see if the remaining bits can be repackaged into a 1U form factor....
Apple had a 1U form factor Mac. If that was a magically highly successive market property they would have kept it. It isn't.
As long as there is a 900-1000W power supply feeding 200-400W of CPU/RAM demands and 300-500W of PCI-e card demands the primary drivers of the Mac Pro form factor still exist if Apple continues to target the same relatively low noise production design constraints.
Waving at trading PCI-e slots for an every larger number of TB ports does absolutely
nothing to alleviate that core design issue.
The Mac Pro should be a couple inches shorts for it is not gratuitously horizontal rack hostile. But there is no "thin"
If Apple threw high end GPU cards and Xeon E5's and high end GPUs out the window then yeah sure they could do a 1-2 slot , at least 1/3 smaller , Mac Pro like derivative with a Xeon E3 .
...and the last step would be to see if TB could possibly in any way be used to network multiple 1U Mac Pros together in a rack for a power cluster.
A workstation trend is for the cluster to move inside the box. Not to push things outside. The Xeon Phi , Nvidia K20 cards, and AMD Firepower 9000 cards can all bring approximately 1TFLOP DP performance inside the box. High Triple digit GFLOP DP performance is doable with more mainstream GPU cards that would likely land in a updated Mac Pro progression anyway. If the Mac Pro cannot participate in that then it will be whipped in the workstation market going forward. If Apple is moving the case design that they will stick with for the next 5-10 years then it needs to be one that tracking the current trends. Not hiding in the flawed "1U pizza boxes will rule the world" past that is out of step with current trends.