Donal Fellows: Prettier. It's amazing what can be done with magical web fonts and bootstrap.js…
kap: Suggested templates for pages based on category (e.g. project, discussion, etc.) to help keep the content looking consistent and expected.
kap: The ability to separate content and discussion where necessary.
JOB: The ability to easily upload image files (drag&drop dialog) and store them automatically on the server (as database images).
aspect: Something like Sister wiki links for manual pages and other external documentation, so they don't have to be tediously, laboriously and belatedly updated to new locations (or new versions).
aspect: Javascript to expand all folded <<discussion>> sections. Finding in-page search results in (eg) string is sucks. The existing markup+js doesn't make this pleasant to do in a bookmarklet.
dbohdan: Page transclusions, meaning the ability to include the text from one page in another. With this longer code snippets could be kept on their own pages with a separate revision history; they would then be included in the page(s) that refer to them like images are now. It could help with #1. Parametrized translcusions ("include this substituting value b for $a") is essentially how MediaWiki solved templates (#3).