Re align: To be honest, I'd love a "keep_align_attr", if it's not too much of a bother for you. Thank you!
Re "big" tag: It was a surprise to me to see it in this author's stories and be made aware of it being problematic in this manner was unpleasant. Few stories I've seen have ever used such a tag, and all of them were on either LJ or DW. As for "other works that use
<big> differently": Hmm. Good question. The only archives I have used to date are ffnet, ao3, tth, wraithbait (and of those I have not downloaded from wraithbait yet), and this is the first time I've seen this tag in action on any of those archives. Personally, I would say that if there isn't a way to get a clean and easy solution to this problem, and if there aren't substantially more people affected, let it be. It'll be a pity, but the epub version is readable, and that's plenty. (Out of curiosity, what about having the option of removing "big" altogether" like with align if it's unsupported anyway? Doable? Not worth the work it'd cause?)
What makes me wonder, though, is this: The author has used this tag in other stories, for example
http://archiveofourown.org/works/7606
In it, she has the first letter of every other paragraph big, and yet, this does not pose a problem for the download, be it html or epub. Is it just a case of the tag not being used as often as in the previous example story (The Water Grinds The Stone)?
I'd like to provide more examples for comparison, but usually the stories I download are reasonably formatted (and if not, replace_br_with_p takes care of that wonderfully).
Re conversion of epub: I actually download WIP stories as epub only (because of the update capability you mentioned), and completed ones as html and epub both (because I like html much better - for reading on a desktop or laptop pc, my ereaders like epub best, and the calibre conversion to htmlz somehow never turns out just the way I like it so I gave it up. Maybe I'll try again over the coming holidays.)