If you rely on IntelliJ (or any other IDE based on the IntelliJ platform like WebStorm i.e.) for your daily work and use a touchpad (no matter if the Macbook internal or the magic trackpad) you should not upgrade to Sierra at the moment. The issue is that the scrolling behavior in IntelliJ is extremely sensitive which makes a controlled scrolling nearly impossible. IntelliJ seems to doesn’t know of a way to fix this at the moment and filed itself a radar at Apples bug tracker. As you can find complains from users of other Apps with the same problem as well (VLC and Minecraft i.e.) it seems plausible that the ball on this is in Apples field.
As Jetbrains obviously have done nothing wrong with its implementation to trigger this issue it would have been a good move from them to address the issue to their customers early (previous to the sierra release) so that they could have waited with the macOS upgrade until the problem is solved. If you are interested you can find a discussion about the problem at their bug tracker.
Not knowing how long it will take Apple or Jetbrains to solve the issue the easy workaround for the users is using a mouse as it affects the trackpad only. I use the magic mouse but every other mouse should work fine, too.