As for big "mini" it seems good!
However, I myself would prefer:
8+ Ram slots
There are 8 DIMM slots on the two package models now. With upcoming transition to DDR4 memory's point-to-point connections it is unlikely going to get models that go past four slots ( since there are four memory controllers currently in Xeon E5 ). There will be systems that add buffering logic but that will be additionally expensive.
Over time memory density is going up. The transition to DDR4 will probably bring a bump in memory prices but over medium term it should be reasonably affordable to put 128GB of memory into four DDR3 or DDR4 slots. There are a subset of folks that really need more than that but that is actually more than a two socket Mac Pro can provide at the moment ( in OS X. The OS caps out at 96GB and there aren't large mobs complaining about that. )
6+ Pcie slots, and a few more empty ones in the backpanel to use for cables and card-addons.
Very similar technology trend. PCI-e v3.0 that should show up in the new Mac Pro is 2x as fast as PCI-e v2.0 which is 4x as fast as what the initial Mac Pro started out with. There is little reason why modern cards can't do more. For example modern GPU cards can drive 4-6 monitors instead of just 1-2. External SAS/SATA cards in a x8 or x16 slots could drive 4-6 external disk boxes relatively easily.
Again there will be a small subset of folks who have a large collection of different (and likely legacy ) cards that don't use concurrently. PCI-e expansion boxes work in that smaller context and isn't really the mainstream of the Mac Pro market.
A single Xeon E5 has 40 PCI-e v3.0 lanes. That is about 20x the amount of bandwidth that Thunderbolt provides. Even in a x16,x16,x4,x4 configuration is a ton of bandwidth there. A more pressing issue is to not let a card use just a minor fraction of what the slot provides. Otherwise essentially wasting lots of bandwidth.
I have so far prefered 2 cpu, but with 6-8 cores in a single cpu it may not matter much as long as critical applications make use of GPU?
Intel so far has showed little interest in moving the E5 1600 series past 6 cores. The 8 & up cores are so far restricted to the two or more CPU package offerings. That likely will continue. There is a decent chance that Intel will merge a integrated GPU into the E5 1600 series at some point just as they have done with the more mainstream desktop core design ( Xeon E3 and basic Core i3 , i5, i7 ) offerings.
All the more likely if the software trend continues where "embarrassingly parallel" workloads are shifted to GPGPU via OpenCL as implicated above. Right now Intels iGPU isn't that great at GPGPU computations but that should change in an iteration or two. It would make more sense to allocate the larger transistor budget on those kind of cores rather than a 'large' x86 cores just to do a small incremental bump from 6 to 8 cores.