First, I'd like to say that I've found this add-on quite useful-- it's well done and has replaced the stand alone tool I used to use for saving stories at risk of disappearing. That said, I have a potential enhancement that I would like to suggest.
I haven't read through the whole thread, so this may have been asked in the past, but would it be possible to generate a list of stories to download based upon your follows, favorites, bookmarks, etc... from various websites? I'm personally interested in pulling all my followed stories from fanfiction.net (1200 or so), but most sites have something of that nature. I haven't really found a good method of simply generating all of those as a list of URLs (a couple of unofficial APIs I may try), so I thought I would check to see if you are open to an enhancement.
Ideally, I would just like to put in a user name and not need to bother signing in through the app. This also opens the possibility of finding a user you like and just pulling their list of follows, favorites, or even stories they've written. Lots of possibilities ultimately, though I imagine each adds complexity.