I agree with you to an extent: The IBM PC was not a very elegant design, and other computers certainly had less complexity to them. But there is a point I want to make which defends this choice somewhat:
Newbies like me are more frustrated by thinking there's no path from introductory material to something useful or realistic. Something that's more immediately friendly would be a simplified virtual machine with no or trivial peripheral hardware, like Redcode in Core War:
http://vyznev.net/corewar/guide.html
The death of education is "So What?": "OK, I've learned to play Core War and I know enough to write a warrior that can occasionally beat other warriors written by beginners. So far, so good... so what? I want to program computers in assembly, not play games using assembly programs, so where's the path from where I am now to where I want to be?"
In this case, the pathway from VM opcodes to native opcodes is hardware interface and, while the IBM PC has some funky hardware, it's heartening to know that your code could, in principle and barring emulation errors, run unmodified on real hardware and do something. Not something useful, but you can get to useful. You can ramp up to it, now that you have the pathway in front of you. It might be a long pathway, but it's there.