MacOS – Scrolling Settings – “Throw”

This may be one of those things that is labeled as a "feature not a bug." It's possible that the swiping gestures that are the same as the gestures on Snow Leopard are considered "Legacy" gestures. If that's the case then it is possible that having it "backwards" Is the expected behavior. If it's a legacy gesture then it may be considered to ignore natural scrolling because that is a "new" feature. I'm not saying that's how it should work, if you ask me if you change the direction of scrolling, it should apply to all gestures, not just the scrolling ones. I've moved mine back to the two finger option for the moment. You should file it at http://www.apple.com/feedback to make sure that Apple knows how confusing this is.

There no official specific settings to this, although with command line changes you can turn inertial settings on and off full stop. Unfortunately, especially if you like the inertial scrolling in part, the beth way forward for you is to understand how it works better.

I've nicked this sentence from the ArsTechnica review, as there is no point in re-inventing the wheel:

Finally, Apple has added iOS-style accelerated scrolling to Mountain Lion. The first three swipes on the trackpad scroll as they did in Lion, but on the fourth swipe, the distance traveled within the document greatly increases. This magnified ratio of finger movement to scrolling distance continues as long as the user keeps swiping repeatedly.

If you like inertial scrolling to a point, then perhaps a workaround is to only use it to a point. Stopping after 3 scrolls will prevent you from triggering the increased scrolling acceleration.

It's not exactly what you want to hear, but sometimes you need to work within the confines of the system if you wish to pick and choose which bits of scrolling behaviour you wish to apply or not. Perhaps further preference options will show up in the future (likely as command line changes), but overall you can probably imagine why they have made this change, because it's a good one for most (non-coding) users.