I've added a couple more percentile levels and tried to optimize their distribution.
Skipping lines to speed things up a little
Deflicker now ramps from the first image selected to the last image selected. (initially it just tried to make all the images look like the first one). This should help for scenes where the lighting changes dramatically (i.e. sunset, sunrise). If you have a scene with a pretty static period, then a transition (such as some amount of night sky then a sunrise), you might want to select and deflicker the static period, then select and deflicker the transition separately, so the ramping is smoother, or you may not need to deflicker the static period at all, in which case only deflickering the transition will save you time.
You should be able to use some amount of the various controls that are known for causing flicker such as clarity and highlights, just apply those settings first to non-deflickered images, then run the deflicker.
If you need to rerun the deflicker make sure you clear the tone curve from all images before hand or the script will calculate the tone curve to apply incorrectly (since there is already one being applied).
I've got some before/after sample videos rendering at the moment, will post them soon.