One Note does have this feature. I would imagine that multilevel filing/notebooks would be the foundation of any good note-taking system. But maybe it is just me.
I have been using ONENOTE for about 4 years and I thought I would try Evernote for a year and I did not even consider that Evernote would not be using a multilevel filing/notebook system.
By design most (not all- but most) who use evernote are on the upper end of tech-abilities / non-paperness preferences. Again maybe it is just me, but it would seem that those who are the target audience for Evernote would be interested in a multilevel filing system.
Today will be my last day using my year-long subscription for anything other than to-do list and fairly insignificant misc notes that do not require a filing system until this feature is available. I am optimistic that it will become available because innovation would require it. However, Innovation required it yester-year. Catch up to innovation requires it today.