While I agree that was the case with windows 98 and earlier, I don't find it to be the case with windows xp, at least not if your using ntfs (FAT32 file system is largely where the problem lies). Yes, after a few years it does boot up and shut down quite a bit slower because it can have a lot of extra/unneeded processes to start/shutdown, but once its running its just as fast as the new install. And if you know what your doing, you can clean up the startup config and speed that up as well.
Oh yeah, it was definitely a lot worse with FAT32 (and infinitely worse with FAT16).
You also touched on another reason why I switched to the Mac. You said, "And if you know what your doing, you can clean up the startup config and speed that up as well." I know what I'm doing, but you know what? I'm sick of doing it. Cliche as it is, I want a system that just works.
I spend all day working with Windows machines, and the last thing I want to do when I get home is work on one. It's kind of like how people that work at McDonald's don't want to eat at McDonald's.
I like computers and technology, or I wouldn't be working in it, but I don't want a home system administration kit. When I use the computer at home, I want to program fun little apps (like games and such), browse the web, edit videos, draw things in Photoshop, listen to music, and basically just goof around. I don't want to tweak my registry settings, figure out why that new driver doesn't work, etc. Some people like that stuff. I did at one point, but not anymore.
I take the same approach with my arcade cabinets. I want them to just work once I've finished building them. I set them up the way I want them the first time, and don't mess with the configs ever again. Some people love tweaking their front-ends, upgrading the MAME versions, and all that. Both approaches are equally valid.