Ah yes, well, I wasn't using pull-to-refresh or zooming, so I could justify the change. Given that the lite version doesn't do nearly as much and assumes functionality only on mobile browsers, it is less resource intensive. Turning off the scrollbars helps too, since of course, they have to be animated as well. That alone might make a big enough difference.
I do know that iScroll applies the translate when it scrolls, so it may not make a difference to apply it manually, but perhaps adding it outside of the scroller (i.e., the container that contains the scroller) might help. Uses more memory, but worth a try.
The number tags and the the number of positioned elements directly impact the performance. For example, the app I'm working on had a ridiculous amount of <SPANs> being generated, most of which were relatively positioned (just slightly). Eliminating a 3rd of those tags increased responsiveness massively, and in the end, I got rid of the relatively positioned tags all-together. And then I worked to factor out the need for all of those SPANs (I had the need to detect a specific word that was tapped on), so that the number of tags was drastically reduced. Scrolling was much better. But still not fast enough for my tastes -- which lead me to goto iScroll-lite. Voila, near-native speed.
The other option I was pursuing (and may still pursue) was the CANVAS tag. I doubt that's the direction you want to go, but for me it would have allowed me to avoid the scroll entirely, and it was uber-fast to write to. Only problem was that the text was blurry, so I had to downscale it by about 75%... which made my head hurt. ;-)