Media Mail is only an option if you don't care what condition the books arrive in, which, we find, is not a sentiment most customers share. We tried Media Mail for the first Dungeon Crawlin' Fools release back in 2005 (before APE was involved) and had hundreds of books returned to us, with hundreds more reported damaged in the mail (and who knows how many not reported). Media Mail is for catalogs, phone books, etc., not books printed on high-quality paper that are meant to sit on your shelf forever.
While I don't have any personal control over APE's shipping choices, I would have strongly urged them not to even consider Media Mail as a viable option should they have included it.