This is a big topic, so I want to lay out a big long thread here and get input for what people think will be useful and what should be prioritized.

This post will hold the overall plan.

Glossary

a template is a type of page on the site. A forum post is one type of page; they use a template called "Linear Post". Blog comments are another type, dictionary words are a third, user profiles are a fourth, and so on.
Many of the site's special pages are scripts or static pages, which have code (or, respectively, don't) but use the so-called default template, which doesn't provide any special formatting. The front page is an example of a script.
The real name of the page created when you make a "Wiki" in a Universe is called a "Root Wiki Page". The "Documents" are actually using the template "Wiki Page".
You can see all of Atlas's Octavia macro code here. (Warning: ugly!)

Yet-To-Be-Created Templates

Language Family. This will be functionally identical to what's currently called a Wiki, but won't let you put Dictionaries in it directly. Instead, you'll put Languages in it. Implemented
Language. This will be based on a Wiki too, but live inside of a language family instead of directly in the Universe. It will contain dictionaries and documents. Implemented
Sound Change. This will be a very simple page belonging to a Dictionary that stores the sound changes and triggers used for auto-inflection and auto-addition to descendant dictionaries.
Biography. Basic profile for a character from a conworld.
Event. Recurring, historical, etc. Will go on a Calendar. Including tags for different perspectives.
Calendar. Like any other daily planner, but with custom date format and offset. Will also provide a real-time clock you can sync with the present if desired. (Challenge: leap years. Oh god.)

New Template Interactions

Wiki Pages (i.e., "Documents") will be recursively nestable. (i.e., they'll have children consisting of more of themselves) Implemented
Root Wiki Pages (i.e., "Wikis") may be recursively nestable. (Opinions?) Not necessary; renamed to "Chapters"
Every Universe, Wiki Page and Root Wiki Page will have a discussion page—not sure if I should use Linear Post (forum post) or Generic Comment (blog comment, recursive) for this. Partly Implemented: only on articles so far.
Dictionaries of mother languages will automatically translate and add new words to their daughter languages (according to Sound Change pages) when they are first added to the parent dictionary (a suppressible behaviour)
Dictionary Entries will display an inflection table (defined with Sound Change pages)
implication: Sound Changes will have two types, diachronic and inflectional, and the inflectional types will need to be tagged with lexical categories, order of application, scheme name (e.g. "first declension", "strong verb"—should use Dictionary Categories for this), and display titles; the diachronics will just need a target dictionary name to output to.
inflected forms (i.e. inflectional Sound Change products) will be manually overridable within each Dictionary Entry, to create irregular words such as via suppletion.

More Features for Existing Templates

New fields on Dictionary Entries: "usage", "attested", "etymology". These seem like the most popular free-text fields that could be useful, and should be easy to support with the parser. Suggested by Zontas: "related terms" (will implement as 'one per line -> bulleted list', as with categories) Implemented
Universes will be created with a group applied by default, so that administrative intervention is not required to collaborate. Implemented (Although with a twist: you have to click a button, but it propagates across all documents, so everything's still good)
Expose more per-page permission controls—e.g. "lock editing by other group members on this Document" Implemented—full permissions widget. Maybe too far?
Edit history for Documents. Implemented
Custom alphabetical sort order for dictionaries (? including support for non-single-character graphemes)

Questions? Thoughts? Opinions? Suggestions? Cough 'em up!