Alter inertia scrolling behaviour in Mountain Lion
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.