I second everything in this. I recently switched my note taking to be organized around concept "hubs" with Zettelkasten-esque linking between them, and it's maybe the biggest improvement I've made in terms of organizing my learning. I sometimes cover material a bit slower, but I rarely have a single session now where I don't have some kind of aha moment. This is a direct product of having to explain what I'm learning in order to fit it into my system, a la the Feynman technique.