One thing I’ve considered recently is adding tagging support, which would let you create custom tags like todo, inprogress, and done. That could let you progress an email across those tags as you’re working on it, just like a task manager. Maybe even having a kanban board view. Would that help?
Another thing I’ve been considering is having custom searches that show in the sidebar and let you do things like mark-as-read and notifications. Maybe then I could have a way for one of them to replace the Aggbox, so you can have the Aggbox filter out your tags.