The command line applications now deal with resource forks just fine, starting in Tiger.
It would be nice to see virtual desktops in MacOS X. Oddly enough, I first saw them on a SGI machine and think the interface was superior to what I've seen in Linux. They're definitely a boost for productivity, and that kept me using my SGI machine as a desktop until I switched virtually all my computing to MacOS X, where it remains today.
That being said, what I really love about MacOS X is how it combines the best of the proprietary and open source worlds. I can do all the Unix-style development I want (mainly web server applications) and still use polished commercial email, photo editing and (the huge strength of the platform) video editing applications.
When I started using MacOS X, the great looking fonts were an enormous part of the appeal. I gather now you have similar things in Linux (and even Windows, not that I want to go there). Now, I really love the designer look and feel of Apple's interface, the polished quality of the computers, and the great Apple applications like Final Cut Pro.
I can see someone who doesn't need or care for those things preferring Linux.