First off, the systems need more DIMM slots. Nehalem systems are supposed to have their memory installed in sets of three because of the triple channel memory controller. The Mac Pro systems have four and eight respectively.
Only the very cheapest single socket LGA 1366 motherboards have four DIMM slots and I've yet to see a dual socket board that has less than twelve of them. The Mac Pro's memory subsystem shouldn't be crippled. It's not a big performance hit, but it's not how it should be.
The motherboards for both machines need basic RAID functionality integrated, as far as I know they do not. The X58/5520 chipset supports RAID 0, 1, 10 and 5. Even RAID 0 and 1 would be fine. That way you could run a pair of SSDs in 0 for the operating system and applications drive.
More drive bays. Four drive bays isn't enough. You should have at least six of them in a high-end workstation. Maybe two 2.5" bays for SSDs and then four 3.5" for regular hard drives. I'd have no problem if they dropped one of the 5.25" bays for more hard drive bays.
eSATA is a must. It's the best available external storage interface around. Right now most hard drives aren't fast enough to saturate 1394b but it won't be long before they do. It'll be a lot time before they can clog SATA 3Gb/s, let alone the forthcoming 6Gb/s standard.
Better GPU options are needed, especially at the lowend. The GT120 is a pretty weak GPU, probably doesn't even have enough frame buffer to drive two 30" panels with a lot of heavy applications open. There also needs to be an option for something like a Quadro FX 4800 or CX.
A Blu-Ray option wouldn't be bad. 25GB BD-Rs are starting to be a pretty decent way of backing up large amounts of data.
A case redesign wouldn't be a bad idea either. This one is getting pretty long in the tooth. It's not a bad design, but it could be better.
