Same problem here.
I happen to know two types of software which scrolls lightning fast in macOS Sierra:
- Java based application, e.g. PyCharm
- The "classic" Terminal application
What's in common is that they scroll line-by-line, but not continuously like Safari or Pages.
When I say "lightning fast", I mean when I swipe with two fingers from bottom to top of the trackpad of my MacBook Air, the Terminal application scrolls about six pages, or the PyCharm app scrolls about 250 to 300 lines.
That's totally INSANE.
However, Safari, Pages, Chrome, Sublime Text 3, Evernote, anything else that scrolls continuously but not line-by-line, behave normally.
To fix the problem, here's what I tried one by one, suggested by some expert:
Rebooting to safe mode cost me more than 20 minutes. So DO NOT WASTE YOUR TIME!
On my MacBook Air, Mac OS X Lion was pre-installed, then it was upgraded to OS X Mountain Lion, then OS X Mavericks, then OS X Yosemite, then OS X El Capitan. None of them caused scrolling problem.
Now we upgrade to macOS Sierra, then scrolling problem happens, to a large group of people, to some specific applications.
So this is DEFINITELY A SOFTWARE PROBLEM of macOS Sierra. NO EXCUSE.