I am - reluctantly - transitioning from IBM Notes 10 to Outlook and OneNote, having started using Lotus Notes in 1993 with Version 3.  Notes is still the best app that I have found to seamlessly integrate email, calendar, todo and note-taking - but HCL won't sell me a single user license (I'm retired).
 
So on to OneNote.  With the addition of Onetastic and OneMore I have been able to import and reformat my data to somewhat replicate the functionality that I had. There one big functionality missing:
 
In Notes you have the ability to file a "Note" (anything) under multiple folders, such that when you open a folder of notes and edit the note, your edits show up no matter what folder you find that document in. Folders (Sections) are logical groups of documents (Pages), not a 1:1 "physical" relationship. 
It appears that OneNote has a similar database architecture in that each Page has a unique ID (I've been playing with Onetastic macros).  So I imagine that sections are simply an array of Page IDs.  It seems it should be relatively easy to allow a Page to exist in any number of Sections at the same time.  All that's needed are 2 new commands - Add and Remove.  "Add" a page to a section (without removing from another section) and "Remove" a page from a section.  "Remove" would have to check if it is removing the Page from it's last Section, to not have orphans, perhaps in effect making it a delete, with appropriate user confirmation.  Move and Copy would retain the existing function - "Move" is simply a simultaneous Add to one Section and Remove from another (leaving any other Section entries alone), while Copy creates a new document altogether.  Delete would of course remove the Page from all Sections.  Going a step further, Section Groups are also, presumably, an array of Sections, which also have unique IDs - so the same functionality could be added for Sections.
 
It might be argued that Tags are a way to accomplish an aspect of logical grouping of documents, but usage is clumsy.  The Section/Page structure is easy to navigate!
 
This functionality would not change existing use of OneNote at all, in fact people could ignore it quite happily.  For those who discover it's incredible flexibility it would set OneNote apart, and make it a strong competitor to HCL Notes!
 
A further powerful enhancement would be to integrate it more closely with OutLook than the simple "Send to OneNote" that exists today.  An option to use the OneNote database for OutLook instead of .pst format would be amazing - then calendar entries, emails, meeting notes, etc. could be organized under Section(s) together...