@Hitch - that's what the new report will show - all characters regardless of where they are used as long as they are visible. Oh, and if you are pasting individual files into the program - why don't you just Merge all the files into one then copy and paste 1 file into it.
@JSWolf - the report will only show the individual characters that are in the book. From Jellby's description it would be up to the font shrinking program to determine which 2 or 3 pair character sets could/should be turned into a ligature. So feeding it just a list of the single characters that appear in a text would be useless for determining ligatures - you would have to feed it the actual text.
Although Jellby requested the report primarily I think for font shrinking, the report is also just another piece of information you can check to see if there are unexpected characters, etc.
As for displaying each character per font, that as Toxaris has said is a much more involved challenge. Its not something that will be in the next release. It should be possible to get the text for tags using a specific class, but checking what font is used by the class is a bit unknown. None of this would help with ligatures though without the full text.
I'll give it some thought, but without a font shrinking program to shrink the fonts it doesn't help much. And if there is already a program to do font shrinking on an epub from the beginning, there doesn't seem to be much of a need for it.