RAM,
4 DIMM slots per CPU package is perfectly aligned with the future Xeon E5 move to DDR4. Single controller per DIMM slot. 4 controllers, 4 slots. This is pretty much pruned as far as it can go unless start pruning off x86 cores (i.e., cap the Mac Pro at 4 cores). Pruning x86 cores is an extremely dubious move at these price points.
Unless Apple is going to start moving whole Mac line up down to lower price points then abandoning these price points don't make much sense either. ( Besides the 27" iMac has four slots. The 21.5" iMac doesn't have four slots for any good technical reason. It is more vanity (can't let folks see RAM door) and/or bad packaging by Apple. It is also a bit of artificial product segmentation to push more folks into the 27" model.)
optical drives,
At least one likely tossed. The fact that many configurations posted here have 2.5" and 3.5" drives stuffed into the 5.25" bay only points that even the users are aligned with two ODDs bays is too many. However, that directly points to the space needing to be repurposed; not removed. This is actually something Apple is grossly behind the curve responding to.
Both 5.25 bays? I'm sure there would be much wailing but yes it is possible. Either a Xserve like sled ( so could service from the front without opening lid) or two transverse mounted 3.5" in the upper bay would likely get more traction over time. ( could move then out of the PCI-e card zone for more room. )
and 3.5" hard drives (in favor of 2.5") all seem like good candidates for cutting.
I can see 3.5" number going down but not down to zero. Most Mac Pro users want a SSD in the configuration. That is easily done with a 2.5" drive sled.
Possibly also dual processors?
Over the long term, the Mac Pro is doomed if a healthy variety of software that scales by core does not show up.
if the bulk of the software doesn't scale then 4 cores is going to be enough. 6 or 8 cores isn't going to matter much either.
Most of the embarrassingly parallel code will drift to GPGPU cards. But there lots more code that either has a mix of scalar and embarrassingly parallel code or users that run multiple program concurrently.
What has been lacking is applications with a the mix of OpenCL and GCD usage. Over the next 5-10 years apps built to leverage the combo of those should grow. If not then the overall Mac platform is in deep trouble.
I think the chances of Apple dropping dual processors are less though. More likely seems like introing a low end with an i7 maybe.
There is small possibility they could split the Mac Pro into two boxes.
At least for the short-medium term, an Xeon E3 would be a better fit with Mac Pro. More PCI-e lanes than a mainstream i7, ECC memory for double/triple digit RAM installs like the rest of the Mac Pro, and not particularly catering to overclocker crowd (take risk out of long term hardware support coverage). Thunderbolt is still trivial to implement as with an i7, so probably can do a typical Apple margin (30+% ) offering near the $2000 border with that kind of box.
The "extreme" i7 models don't buy anything significant. They cost exactly the same as the E5 Xeon models. They run just as hot TDP wise so the size of the box being driven by that constraint isn't any better. Using Xeon E5 1600 and 2600 CPUs allows for shared infrastructure and component costs. i7 throws that out the window for almost zero net benefit outside of tinkering flexibility.
All those things also nicely dovetail with getting a Mac Pro more rack friendly.
It doesn't have to be rack friendly, just not rack hostile. It is primarily just the handles that are the problem. They have absolutely nothing to do with the device functioning as a computer. Cutting into the storage and computational functionality because of the handles is horrifically bad design.
Modest adjustments for shape but keeping the same volume would make the it neither friendly or hostile. It would still be a little quirky, but much less a gratuitous pain.
A smaller box has far more synergy with being on top of a desk instead of nominally being targeted for the floor (or optionally a rack). With Thunderbolt and targeted at actual desktop would make it more aligned with the "tail wagging dog" position of pairing it with the Thunderbolt docking station (Display). The dangling MagSafe connector would still illustrate that it is a contrived configuration, but it far less contrived as the Mac Pro sitting on the floor and the TB docking station not being able to reach flexibly.
Apple delivered MBA along side MBP so maybe they'll do two versions for several years. It is a bigger risk than they have done previously.
(I also think compatibility with the new wave of PC EFI cards is on the list. Making it so Apple doesn't have to make special cards takes some of the development costs off the Mac Pro.)
That has also been an inhibitor to the Mac Pro market. If the value add of the box is being able to insert PCI-e cards to then minimizing the size of the PCI-e card market isn't going to help. With Windows 8 being UEFI by default it looks like the rest of the market has caught up to where Apple is.
If Apple can get the Mac Pro back on a positive growth path then 3rd party vendors will likely contribute to the ecosystem.