The disadvantage of an "all search" solution is that it presumes that you know what you are looking for. Some of the greatest value I get from my notes happens when I'm serendipitously browsing an old hierarchy, remembering connections I made before.
All search plus some form of spaced memorization scheme for pages or blocks within pages would be nice, I wouldn't have to actively structure my notes that way. I hate structure, I'm always refactoring, so I prefer just saving things in one big folder with labels if I can. I wish I didn't even have to use folders in my file system!
