I agree it would be very helpful if AS2 could save the largest subset of frames as a separate file. So if you picked 1000, 2000, 3000 frame stacks it could just save the 3000 best along with a text file that describes the content (original file name and selection criteria). Oh and I'd still like a 'project file' capability that saves all settings. Essential for knowledge sharing among other things. Sending around screenshots with the settings is a bit archaic.
It's actually pretty easy to use PIPP for this type of preprocessing and AS2 and PIPP seem to agree generally on quality.