I'm still trying to find a foot-hold on how to reorganize it -- I completely reorganized my anthro TH, and might try to do something similar..?
So far my ideas for folders would be
 Active Stories > Pokécalypse ; PMD.... etc. (I'm realizing a lot of my stories are unnamed or don't have titles LOL, there's way more than just the two.)
    I might make it so PMD is sorted by place -- such as "Treasure Town" and "The Guild" (Just example names, I plan to have a different town name)
 Blogs > Sorting by blog name (But, perhaps I will instead tag the characters by the blog name and then have them sorted into different folders..?)
 Sorting (Designs I have to sort into stories still) > Mythics

& then having them sorted in Flattened folders with Trainers over Pokemon (Just because there's usually less trainers)

I still don't know what I'll be doing with Iron Petal & Jellicate -- Originally, I had planned to make them some sort of open species sort of deal (as they're fakemon) but I'm not sure atm if I'll keep it that way. I might give them different tabs for different kinds of OCs that are that species?
Either way they'll probably end up in sorting for a while.