I'm using xubuntu (not unity) and mouse scrolling works totally wrong. I see first comments on this dated 2011. Now it is 2017 and everything is the same mess.
So. I'm using xubuntu. And I like natural mouse scrolling direction - the same way it works in MacOS X. If you want to move your page up you scroll two fingers up. If scroll down then down.
I have touchpad. By default I have reverse scrolling direction. Scrolling fingers up scroll page down, left to right. If I turn on reverse scrolling for the touchpad then I get natural scrolling direction for up/down. But left right direction is still unnatural. And separate issue is google chrome (not chromium, I didn't check it). My Chrome version is 58.0.3029.110 (64-bit). And it totally ignores system settings. It has always unnatural scrolling direction for up/down.