I have a Logitech VX Nano and a MBP running Sierra 10.12.1 (16B2555). The problem isn't that mouse scrolling is choppy or slow, the problem is anything but a rapid 20%+ turn of the scroll wheel is completely ignored. I'm also able to turn the scroll wheel as far as possible very slowly and not have any scrolling occur. When using this mouse on other OSes, the slightest scroll wheel turn will result in a proportional scroll on the screen.
I was having this problem in Mac OS 10.12 and 10.12.1. I searched and could not find a good answer related to this. I did upgrade to 10.12.2 a couple of days ago and, even though there is no mention of changes related to mice in the release notes, my problem went away.