I have found myself evolving to the same approach. One important point you make is, ‘so I’ve taken to using it more for simple notes’. There is no shame in “simple notes!” A tendency with app developers is that as soon as it has a decent text editor, it aspires to be a do-it-all writing platform. I think Bear fell into this trap.
Right now I’m positioning Ulysses for larger scale writing projects that I want to have permanence, and Agenda for “simple notes” that will may evolve to a larger-scale project, in which case they “move” to Ulysses (or some other app), or that have some chronological significance, in which case Agenda is really serving as a notebook that preserves that timeline.
Just when I reach a point at which I’m tempted to stop using Agenda and do everything in Ulysses, I realize that I still have a need for “simple notes.” As long as Agenda stays focused (which the developers keep acknowledging), I think there’s purpose for both apps.