I kinda agree with your point, and hate spending time organizing or following some "system" for my notes. Search is great, and is the thing that almost killed my paper notebook.

However, one feature I would really love to have but never seen, is a combined todo - notes app.

I often jot down notes as in "things to note / remember", but also, in the same flow, I'd note thinks I'd need to do. I would love to be able to gather those automatically in a view, and be able to see them as done when I revisit the initial note after marking them as such from the "todo view".

The closest I've seen was some VimWiki, but I've found that fairly unwieldy (though I love the idea of taking notes in vim).