What I'm thinking I could is this for now... 
Create a manga top level IN the anime subdomain, and then the content in that toplevel (provided there is enough content to support it) will eventually become its own subdomain.  But at least this way, the stuff is already set up and a move would be relatively easy comparatively. 
When I do this, I'll set it up with the usual misc categories and what not, and when you and others you know need a category for a specific fandom, tell me what it is and I can that going as well.  It'll be a bit weird as far as set up, because I only have 3 levels to work in, and only two are posting levels.  However, I can uplevel everything once it goes to its own subdomain. 
So, what I'm looking at then for structure is the following, initially... 
Manga-top 
General, Het, AU, etc-2nd level 
alphanumeric cats (i.e. a-f, g-l, and etc) 2nd level 
specific title cats - 3rd level