The one variety of story I don't see mentioned here is that which on
occasion I've characterized as "The Secret Behind the Canon", in which the
"outer surface" is unchanged from the anime or manga but something quite
unexpected is going on below.  The (ahem) canonical example, in my
opinion, is Ranma fanfic "The Masks We Must Wear".  The question that
arises is whether this story type counts as an alternate universe;
however, if you assume that the canonical version of the anime/manga
*isn't* hiding anything, then the hidden assumptions of the "secret"
stories certainly qualify as "what ifs".  Any thoughts or comments,
anyone? 

-- Bob