This is the number #1 reason I'm searching for a different note taking app at this point. I love Evernote, tasks are awesome, and the features work really well together.
But I have a lot of notes across a wide range of topics, and as a one stop shop for web clipping and other things, it's missing stuff.
However the one that is causing me pain is this inability to manage a collection of notes more than one level deep. Make it a paid feature, whatever, I'm a paid member, but this needs to be there... you know, like templates and resizing images needed to be for many years.