Besides using Agenda as my main note taking app for all kinds of stuff, I also moved my todo lists over to Agenda now.
I usually have one "todo list note” in each project plus I have an “Inbox” note for uncategorized things and one “Today” note for things I need to focus on today.
I added a ￼todo￼ tag to each of those notes and saved a search for the￼ tag to the sidebar. Like this I have a pretty good overview over all my tasks, or for more focus, I can put some of those notes “on the agenda".
I actually love the fact that Agenda is NOT a todo app, because it lets me rearrange the todos as I wish and add notes and text anywhere, as it’s just text and editing text is quick and easy. The structure that todo apps impose is often limiting and then I tend to fiddle around more with the todo app instead of being productive.
One feature I could imagine though would be to automatically extract todos/checklist items from notes and show them in a central place. I recently discovered that Dropbox Paper does this, while remaining “just text” as well.