Break things up into atomic facts. Build rich hierarchies of interconnections and integrative questions. Don't put in orphan questions. Patterns for how to engage with reading material. Patterns (and anti-patterns) for question types. Patterns for the kinds of things you'd like to memorize.

Of course, instead of using Anki I could have taken conventional notes, using a similar process to build up an understanding of the paper. But using Anki gave me confidence I would retain much of the understanding over the long term.