In order of expected difficulty, some ideas off the top of my head:

Toothpaste for Wakaba. More stylesheets in general. Make thread replies line up consistently instead of clearing the parent's float and staggering - makes for easier visual separation of threads. Time zone pref so times are reported in user's preferred time zone. Or, at least, "current time is" so I don't have to try to figure out what time zone the timestamps are in. "Ignore thread" option. Virtual board "/my/" where you can save threads/images you like or want to track. "NSFW" flag (will require active moderators to be effective).

Does wakaba already have an administrative option to set size of thumbnails? They are rather large across wakachan sites - smaller=less bandwidth.

OK, so some of those are "fundamental changes".