The built-in terminal is basically broken:
-page-up and page-down don't work unless you hold shift
-It uses CTRL-C instead of Command-C, unlike the rest of the OS.
-I still can't find hotkeys to jump to the beginning of end of line, or skip over entire words (home, end, ctrl-arrow in Linux and Windows)
Home and End are COMPLETELY USELESS on OS X. I have never, in decades of computing thought "Oh, I want to scroll to the top or bottom of this document with one keypress, but not even bring the cursor with me." Given how often during programming I want to select an entire line, this is broken.
The mouse acceleration is stupid. I know you can get used to it, but then try to play StarCraft or something on it, and you will be awful (or at least severely handicapped), because the mouse acceleration system just doesn't work for stuff like that. Also, Lion broke all the work arounds.
The XCode debugger doesn't let me inspect anything that even might be out of scope. Most of the inspections are useless anyway. You can't even see a list of what is in an NSArray (isa = Class, puh-lease).
Viewing hidden files in Finder is hard enough to not remember. Viewing hidden files on a remote server seems to be impossible (maybe it isn't, I don't care). Simply typing in the folder you want to go to is a huge project.
OS X is a poor network neighbor. It rarely detects my other machines, and when it does it's after waiting forever, and it still barely works.
And, oh yeah, it cost me as much as my other 3 computers combined and is the worst of the 4, spec-wise.
I'm surprised Ctrl-C is a problem for you, especially since you come from a nix background. I'm super ok with it, especially since Cmd-C is the copy command.
Mouse acceleration does suck. It's directly led to a big decrease in the number of amusing photoshops I make; on the plus side, I've started using the keyboard much more.
I haven't had any issues showing hidden files; I just always show them. Going to a specific folder is as simple as either Cmd-Shift-G or typing "open /Some/Folder/Name" in terminal.
You make a lot of good points. I hated OS X at first, but I got used to it; I could probably move to a nix machine, but there would definitely be a long and painful adjustment period, much as there was for you. And as far as the cost, I'm paying for the OS X design, not the hardware - something not everyone agrees with.
Agree with everything. Mouse acceleration curve is the deal breaker for me because I couldn't get it close to Windows feel. The pointer slowdown is too sharp at the end of your mouse move, the pointer itself gets jerky and jumpy when tracking over a small area.
I've tried various free and paid tools, but no joy (OS X Lion). Funny that I have no such problems with trackpad, but maybe that's attributed to myself appreciating the trackpad too much while using it because every other one I've tried sucked unbelievably.
I frequently want to scroll the display without moving the cursor. As for selecting lines, you do realize that Ctrl+A and Ctrl+E work everywhere in OS X, right? Generally whenever I select an entire line, I do so to erase, move, or duplicate it, and Cocoa's Emacs-style shortcuts are much nicer than Windows/CUA-style shortcuts for these operations (and difficult to support on systems where Ctrl is used for menu command accelerators).
Far more frequently, I want to delete from the current cursor position to the end of a line, and Ctrl+K is much nicer than Shift+End, Backspace.
As a full-time Linux/Django and iOS developer, switching over to the Mac from Ubuntu is f'ing painful.
Linux's reputation is far worse than it deserves.