I enabled natural scrolling by creating a new entry in Startup Programs ince I'd hate to have a useless icon in the panel all the time. (used http://agoraphobiae.wordpress.com/2013/02/05/inverted-scrolling-and-two-finger-scrolling-in-linux-mint-14/
) to figure out the command, then created a new entry with Command: xinput set-button-map 9 1 2 3 5 4 7 6).
It mostly works perfect. Unfortunately, yes, some Mint applications don't get it. The System Settings window scrolls correctly, the Background Settings window scrolls incorrectly. Software Manager scrolls correctly, Nemo scrolls incorrectly. It's weird!
Since I use a trackpad, natural scrolling really feels right. I'm really looking forward to when Mint adds proper support for this.