From what I can see, there's a bit of a two-fold problem here.
On one hand, the Fiction section modification's limitations do not allow readers to physically browse listings by genre,fandom or other tags.
On the other hand - a great number of authors either don't understand the system well or care enough to add that information to existing or even new entries in order to make the search function effective.
As far as solutions go, one thing mentioned above - manually creating an index... that was done before would be very time consuming and would probably work out if there were a number of volunteers willing to dedicate their time and energy to an endeavor like that again. If the threads from the old system still exist - that might be a great place to start but chances are, it would eventually become obsolete... for the same reasons we have this problem now... I think?
I'm not familiar with vBulletin - but I'm fairly certain that the Fiction modification... well, that's probably as advanced as it's going to get.
Since the Fiction section has become such a significant (I'd venture to say - important) part of this community, it might be worthwhile to implement Directory of fiction on site. It is possible using a component built for Joomla CMS - the CMS that drives the main aarinfantasy.com homepage.
The benefits of that would be a single entry could fall under various categories/sub-categories, which makes it easily browsable and searchable as well. Any registered member of the site could add entries to the listing... the owners/writers are able to claim a listing even if they didn't add it to the directory themselves, etc.
The drawbacks to suggesting something like that (ie: the reason the staff would probably not go for it) are:
1. The component is not free
2. Would still take staff's time and effort to implement.
3. It would be separate and completely independent of the Fiction section. All it would be is a directory.
4. If people wouldn't make use of it and submit listings - it would become obsolete as well - and be a total waste of time, effort and money.
I have one particular component on mind - which can be seen in action here:
(sorry for posting a link to my own site - it's just for an example/demo purposes only. Feel free to remove the link! if it's a problem)
It's not the only viable option out there though, I'm sure.
I guess what I'm really getting at is that any solution to be considered will require time and effort of both staff and other members of the community.
Maybe the first thing that should be determined is how important the Fiction part of the site is to the community as a whole - and how much we're willing to do collectively, to keep it alive or make it as beneficial as possible to writers and readers alike..?