Re:Why? (Score 1)

All valid points, maybe this will help.

1. Very true, but Apple is a hardware company first and foremost (and most people feel that it's their strongest area). You can't buy a Mac and expect to slap in the latest nVidia and have it work out of the box. Hopefully this changes as time goes on.
2. Fink fink and more fink. Check out the Fink Project if you haven't already. It will allow you almost all the flexibility you need from point #2. The only real setback is that you can't boot into KDE or Gnome, but you can run it in an X window.
3. I'm with you here - OS X security and a Unix core brought me to Apple, and their response to a real issue pissed me off. Again, as market share grows, let's hope this trend reverses.
4. Fink again, if you don't want to go the VM route. Also, Eclipse is most certainly available in OS X (use it daily).
5. You're right, this is a preference thing. I spent my entire life on Windows and Linux, hating Apple. Then 10.2 came out, and I couldn't imagine working as productively in another environment again. It's a mind shift away from Linux DMs, and if that flexibility is necessary, you'll find OS X a pain to work around.