I could be wrong but i'm pretty sure thunderbolt connectors have a shorter distance than USB 3 placement wise away from the thunderbolt controller on the PCB.
Yes, this. The Thunderbolt controller has to be very close to the physical ports. That is likely going to be mean that there will just be at most two ports on the back. (if any at all.... it is still a "solution" in search of a core problem the Mac Pro doesn't have. )
Probably the least disruptive way to do it would be to drop the two rear FW800 ports and replace them with Thunderbolt. Apple could leave two on the front for those who wedded FW without need of a dongle.
Dropping Ethernet ports is loopy. If anything, Apple should be trying to move to 10GbE ports instead of dropping them. TB-> 1GbE are a tolerable kludge if necessary but on the Mac Pro that isn't even remotely creditable. The Mac Pro is 5U wide. You'd have to be on Apple crack to buy into the notion that "needed" to go to TB dongles for Ethernet to "save" width on Mac Pro. For "thinner than a inch" devices yes. For multiple inches thick devices .... it will be around for a long time.
I would guess it would go like this (presuming adding TB )
Front:
2 USB 3.0 (or maybe just one depend upon how many hubs they insert.)
2 FW 800
1 headphone jack + speaker.
Back:
2 Thunderbolt ports
2 USB 3.0 ports
2 1GbE ports
Optical digital audio input and output TOSLINK ports
Analog stereo line-level input and output minijacks
I expect Apple to dump USB 2.0 before they dump FW800 or Ethernet from the Mac Pro. I think they will generally avoid USB ports with color coded inserts to distinguish between 2.0 and 3.0 sockets. They just make them all 3.0. That will have a side effect of limiting the number of USB sockets. Those folks that need a bucketload of USB 2.0 ports will be pointed at TB expansion docks. Four is plenty especially in the context that most monitors have USB hubs in them.
It shouldn't be too hard to move the FW controller to the front of the motherboard closer to the remaining sockets. It wasn't like there were multiple FW controllers in the Mac Pro anyway ( if I recall correctly. It was 4 sockets on the same controller, which actually has limitations.)
While Intel has a new "more affordable" 10GbE motherboard controller now, I suspect Apple will not get it for a price they would like on this first iteration. It would be 'nice' if Apple helped move standard workstation networking to 10GbE. They are more likely to be tailing edge adopters there. (all the more so since 10GbE will somewhat compete for somewhat limited E5 1600 PCI-e lanes. )
What I mean by this is if the trace back to the thunderbolt controller is longer than X then how would Apple place a daughterboard on the front for thunderbolt connectivity? I don't know if any manufacturer has a thunderbolt in case design?!?!?
There are several designs. The issue is moving the Thunderbolt controller to the edge... not the draughtboards. The daughterboard is just the source of the PCI-e lanes. Those don't have a 2 inch limit. Largely because the bandwidth is broken down into more lanes PCI-e . Thunderbolt basically has two "lanes" going out and the path to the TB controller is 4 PCI-e lanes.
The one quirk that Apple may run into with the daughterboard is that PCI-e v 3.0 is twice as fast as v2.0. The almost 90 degree turn the perpendicularly mounted daughterboard makes isn't so hot for the v3.0 signals any more than tend bends are unfriendly to TB controller to port connections.
Edit: This is from anandtech -
"As Thunderbolt carries more bandwidth than USB 3.0, trace routing is very important to achieving max performance. ..."
http://www.anandtech.com/show/5884/...part-2-intels-dz77rek75-asus-p8z77v-premium/1
[ NOTE: the 8 USB 3.0 ports on the Intel board are really provided to two internal hubs that are connected to 2 USB 3.0 supply lines. Block diagram in the ]
Toms hardware has another decent overview of some of the low level issues. ( namely how controllers bridge bandwidth )
http://www.tomshardware.com/reviews/thunderbolt-performance-z77a-gd80,3205.html