At work I literally have a Mac laptop, a Linux desktop, and a Windows desktop. Three machines. I develop java software.
About (1)... Let's agree that Apple did it right. The control key is interpretted by Mac, Linux, and Windows to create the control characters in ASCII. Open a command line window on Mac, Linux, and Windows. Hit control-h. All of them do backspace which is what control-h is in ASCII.
control-c is suppose to send a process an interrupt. Works exactly right on a Mac in a terminal. Works right on Windows in a terminal. Works right on Linux in a terminal. Not look at other applications. Macs don't reuse the command. Copy is command-c. Control-c is ignored. On Windows it means something totally different. Control-c now copies. Linux like lemmings tried to have it the Windows way so control-c copies unless your in a terminal window and then to copy you've got to do control-shift-copy. I have no problem going from Mac to Windows. Takes a little getting used to but they are self-consistent. Linux which tried to do it the Windows way creates a problem.
(5) I hate on Windows having to decide whether what I'm looking for is a file or a directory. Alphabetical is a nice system. Don't have to keep wondering whether what I remember to look for was the directory name or the name of the file.
What OS X Could Learn From Windows