Yes, upgrades that aren't Thunderbolt-devices will be difficult. But as others have pointed out, most people don't upgrade, and when they do, so much needs to be changed anyway, that you're almost better off buying a new computer.
For example. I built a Sandy Bridge based computer in January 2011. Two and a half years ago. If I wanted to upgrade to the newest line of CPUs, I'd be forced to buy a new motherboard as well as CPU, as the Haswell isn't socket compatible with Sandy and Ivy Bridge (nor are AMD CPUs). Fortunately it still supports DDR-3, so I wouldn't have to upgrade that though.
But pulling everything out of the case, putting in new hardware, reinstalling drivers, the inevitable bitching from Windows about how I'm a damned, dirty, filthy software pirate for upgrading my hardware really doesn't seem worth it compared to simply buying a new computer.
And if you work in an office? I don't think I know any people who does works in corporate IT, who've upgraded internal hardware - they generally buy new stuff when the old stuff doesn't cut it any more, or when new stuff makes it economically viable to upgrade due to time savings.
And considering the cheapest Mac Pro available in the Apple Store at the moment is $2,499, I don't think this is aimed at home users either - they'd be going for iMacs.
Equally upgradable (or lack thereof), but if it works, why bother?