Thought I’d copy and paste this from UserEcho because it’s getting no exposure there and it’s a sore point for me when using ST2. Hopefully other Mac users will see this thread and vote!
In OS X, when you click on a backgrounded window the window typically gets pulled to the fore and does nothing else. Currently in ST2 clicking on a backgrounded window will change your selection etc. in addition to pulling it into the foreground. This annoys me frequently as I’ll lose my multiple selections or I’ll scroll the window when I click on the minimap.