At the moment I have mine set up to always prompt for the category. But how about this: the first time you add a word from a document you get a pop-up asking you if you want to use your overall default category, set a specific category for this document, or choose a category manually each time you add a word.
A few other suggestions (you know, just in case you're not busy or anything): could you make it so that when you return to a list it remembers your last position rather than returning to the top? I have some quite long lists, and I've often found myself adding a word from the reader, going to the flashcards to edit the entry, returning to the document reader and then having to exit and re-enter the flashcard list when I next add a card, and having to flick back down to the bottom every time. Another possibility would be to have the list check to see if any new cards have been added when you return to the list from an individual card.
And finally, how about the ability to create some sort of practice routines/workouts? I tend to do the same kind of routine every time - first a fill-in-the-blanks headword test, then a fill-in-the-blanks on pronunciation, then both again with a different list, then a big tones test on both lists, and finally another fill-in-the-blanks headwords focusing on words I've got wrong in the past. It would be lovely if I could set it up to run that for me automatically without having to fiddle with the settings in between each one.
Not that I mean to sound as though I'm dissatisfied with the software as it is...