It also uses custom fans (a peeve of mine), a crappy PSU (have had problems with smelliness and failure), and hides 2 of the damn SATA ports (?? WHY?!).
A lot of people don't have problems with the PSU, most of them are fine. In the pc world you have the same thing: some will complain that the PSU is a piece of crap, others are happy with it. The sata ports in the 2009/2010 Mac Pro models are easily reachable unlike my Sun Blade 100.
The custom fans however are quite a problem, especially when you want to replace them when the machine is, say, 5 yrs old (it would be nice if getting spare parts is as easy as getting a new Mac). It doesn't make sense to use custom fans, there is not much you can gain in this area.
I also hate the fact that some PCIe cards don't fit or are like 1 micron away from the bottom compartment/wind tunnel--impeding air flow and limiting card selection.
That seems to be a problem with hardware manufacturers in general. Some do it just a little bit different causing things to not fit in some computers. It is annoying as hell

I don't think it does affect airflow all that much (a small gap isn't going to do magic on the airflow so closing will not make the machine/component a lot hotter). I think this is nitpicking.
Edit: oh yeah, and it's proprietary as hell--can't replace the mobo except with another Apple mobo...and it takes a life-age of man to do it.
Just like IBM, Dell, HP, Sun/Oracle, NEC and many others. The Mac Pro and similar machines from competitors are all proprietary custom build machines with the option to upgrade parts of it (mem, disk, videocard, PCIe expansion, cpu) but not everything. These kind of machines will come with a special service contract which the Mac Pro doesn't (AppleCare is not even remotely close to such contracts). That is the Mac Pro's biggest minus.
Edit2: and it's not that sturdy! I've had cheap PC cases dent less when dropped/impaled.
Good point!, dropping cases is something we do daily!1!11!!! </sarcasm>
The machine as a whole is as sturdy as other similar workstations. The plating is a bit thicker (about 3 mm) but that's it.
oooooh now you're talkin.
Well it's comforting to know Apple's still ignoring me after all these years.
It's even more comforting to know that the competition is doing the exact same thing. Hot swappable sata drives is something that is more useful on a server than on a workstation. Which is why not every workstation will have it. There are still even some operating systems that simply do not support hot swapping. FreeBSD is one of them (they still use the old style /dev so you need to scan an initialise manually) which makes zraid (part of zfs) less easy. If you want hot swappable drives you need the hardware and the software support for it.
I've never cut myself on a sharp metal edge. (big plus if you're hands are in cases all day long).
The same goes for a lot of other cases. You need to watch out for the cheap ones, they're made of tin or something (you can cut yourself really easily with that material).
Complaints:
-Lack of USB ports. What isn't USB these days? It has 5, but the 2 on the front are useless for anything permanent.
The only thing I really dislike about the Mac Pro's hardware. I bought a PCIe USB card to resolve it but I shouldn't have had to. Installing the card is really easy with the Mac Pro.
-Lack of support for graphics cards
-Lack of support for processors (there is no reason the 2010 firmware can't work with the 2009 and then I could use westmere processors, but Noooo!!!)
I think those 2 boil down to something more general: there isn't that much 3rd party components you can use without problems in Macs. In the current iMacs you need to watch out when using a 3rd party ssd, with the Mac Pro it's the videocards and cpu's. I wish Apple would offer more videocard options and made it easier to buy something like the processor tray. Other manufacturers sell such replacement parts.