OS X may not be your cup of tea, and that's just fine. You just happened to attack what I perceive as one of its strengths, so I'm surprised by your choice of targets.
Although I was a bit skeptical at first, once I got used to the concept it made a lot of sense. On a Mac, Ctrl+key combos are for contextual menus in the GUI and navigation/commands in terminals and text areas. For instance, you can navigate to the beginning and end of nearly any text element in OS X by using Ctrl-a and Ctrl-e, the standard Emacs shortcuts. And the Cmd+key combos are for GUI and application-level shortcuts, such as copy, paste, print, close, etc. There are two different contexts being handled, so it makes sense to use a different key. The combo to copy a line from a terminal window should not interfere with the combo to cancel the running process within that window, as an example, and on OS X it doesn't.
Most importantly, those shortcuts are implemented consistently across applications. No matter what app I'm working on, Cmd+, will always bring up the Preferences window, Cmd+w will close the window, Cmd+q will quit the application, Cmd+h will hide it, Cmd+p will invoke the print dialog, Cmd+s will save, Cmd+S will save as, Cmd+z will undo, etc. I never have to stop and think about it, or get jarred out of my train of thought by an application that uses some non-standard shortcut to save, or quit or similar. I use Ubuntu at the office and while many apps are making good progress on presenting a consistent interface across the OS, I still get frustrated regularly by apps that do things differently.
Finally, Cmd+Tab provides the same functionality as Alt-Tab on Windows and Linux. Cmd+` lets you switch between the windows of a particular application, which I've found to be quite useful on a many occasions.
Point being, don't knock it till you understand why others like it. While I don't agree with all of Apple's UI decisions, there are plenty of excellent usability features in OS X and I now prefer it to both Windows and Linux because those features line up nicely with the way I work.
Aside from a few crappy lowest-common denominator Java desktop apps that haven't been optimised for OS X, but thankfully those are disappearing fast.
I really see no serious UI benefit in Apple's products. It seems roughly equivalent to me, and it uses the same paradigms as other conventional systems, it just does it in a shinier way, and it seems cool just because Apple does it, just like everything MTV does seems cool to a teenager.