This is so true. I bought a PowerBook 15" assuming that swapping ctrl and caps-lock would be a no-brainer but it turned out to be a real headache. I'm using uControl now, which does a decent job but it feels like a bit of a hack, since it won't let me remap caps-lock to ctrl. (caps-lock has its uses when you do a lot of programming.)
Then there's the stupid annoyance that there's no way to make the function keys act like function keys without holding down the fn key!! uControl offers an option for this but it won't work for F5. Come on, Apple, you had to figure that this would annoy a pretty large number of people! Would an option in System Settings be so terrible?
The worst HID nightmare, though, is the nasty mouse acceleration that Apple forces upon you. Fine mouse movements are painfully slow, while fast ones are uselessly fast. Again, how about a "Disable Mouse Acceleration" option, Apple? How hard would that be?
I never imagined I would say this, but switching from X11 to Mac OS X has been a definite step backwards in basic comfort and usability. The hardware is slick, however, and I'm not afraid to hack the software into shape, so I'm a switcher. For now...