Full unix compatibility without easy, comprehensive & working BINARY package management (like debian, or archlinux) is still a big pain in the ass. Setting up something like the mysqldb library, mod_python, apache, and django can be a 1 hour production vs. the 5 minute production that it is on linux.
Agreed, package managers are a godsend. That's why there's http://www.macports.org/ and http://www.finkproject.org/
Then a good friend of mine convinced me to get an iPhone. I was hesitant at first, but after trying one I decided to go for it.
Then I got a job where my choices were a MacBook Pro or a Dell with Vista. Three guesses which one I took (the first two don't count).
I must admit OS X is really nice, and full Unix compatibility is a huge plus. Still... sigh
[Edit: missing period]