I've figured out why I was having such a hard time organizing things here. Turns out, things like "Neurological Mutation" were both a page AND a category, leading to confusion for obvious reasons.
Anyway. What I'm doing at this point is linking a few "root categories" on the front page, and filing everything under them as needed. Right now the root categories are Information, Characters, and Abilities. More will probably need to be added. Under each of those, we have subcategories, such as canon or original characters. Ideally, this will help make navigation easier.
So, my present work is making sure everything we have now is placed in the proper category (I don't think I'm going to add much more until organization is a little better, anyway).
We also seem to have a deluge of extra categories. If you add a category by typing it into the bottom of a page, watch out for typos, or hitting enter will create a new category with a typoed name. Sigh. Well, I'll be getting rid of the extras and hopefully trim everything down to nice and navigable size.