Quote: "Moving the "show desktop" function to the tray REALLY annoyed me too"
Start+D has always been faster, but putting the button in the corner makes it easier to click since you can't overshoot it. Or are you saying you'd prefer to not have it on the taskbar?
Quote: "as did the way running programs are displayed since Win7 (grouped vs the order they started)"
I believe it's possible to disable that behavior, but I actually prefer the grouping now. It also reduces the amount of space used by the taskbar which I move to the left side of the screen.
Quote: "Related to that, there's the right-click to open a new instance of a currently running program instead of just leaving the icon in the quick launch area."
You can just middle click the icon to open a new instance. Or you can shift-left click the icon. Ctrl-shift click will open a new instance as administrator.
[Edit]
My main dislike is probably that it's more work to install/build/use libraries than it is on linux.