What if your classmate missed last week's class and asked you to email her just the notes from Wednesday and Friday? She doesn't want PDFs, because she want to somehow 'merge' them with her notes also in OneNote.
Then you are better of copying them, going through them with that classmate or by creating your own notes from books, presentation, etc. that is available. What you are describing here is not only lazy but also stupid because by doing so little effort the content of the note won't stick. It's a useless exercise.
Still, there will be other occasions where you'd want to share your data (OneNote and the like aren't for note taking in class only!) and you can do this either via PDF (which usually is a very good format because others don't need or shouldn't be able to edit it) or by inviting them. In case of the latter you can simply copy the page to your own notebook and do whatever you want with it. When you put the OneNote notebook on SharePoint or a network drive you can use it with a group without having to share any page/section you create. Simply open the notebook from the location and you're done. It will function the same way OneDrive, Dropbox, etc. do: it will sync the notebooks to your local device. All edits are done in that local copy and synced back to wherever the notebook is actually stored. It will also show you who put a particular part of a note where it is (text, picture, drawing, etc.). You can't do any of this with Evernote or Notability so if you really want to use it with others then clearly you are better off with OneNote.
I am speaking from an instructor's point of view, not students'. I want to be able to share my lecture file in the native format after each class, not as PDFs, with other instructors and students.
And speaking from both a student and instructors point of view: I'd like to use lecture stuff without having to go out and buy the same gear the instructor/student uses just to be able to use their data. PDF is what you should use for 2 simple things: you can lock it down so people can't edit it and thus it will always be exactly the same as how you intended it to be (from a student point of view I can tell you that this is a must have with any instructor as quite a lot tend to read with their mouse and accidentally delete stuff; PDF prevents this) and the other side gets to decide what they use to read/edit the file. Want to put it in OneNote? No problem. Same for iBooks, GoodReader, Evernote and so on.
Btw, Microsoft specifically targets OneNote at educational use and created some special tooling and marketing for this. I find it more difficult to find material on how to use OneNote in a non-education setting. It's one of the things Evernote does better.
My point is, while OneOnte is good for many things, but its notebook organization is inflexible and restrictive.
Or in other words, anything that is an old skool paper notebook and pen is inflexible and restrictive because OneNote is based on good old paper. Notebooks in OneNote are the same as those physical ones (or binders). Sections in OneNote are the same as in those notebooks or binders and pages are no more like actual sheets of paper. That's why a lot of people use OneNote: it has a very easy to grasp way of doing things because it is no different than ordinary paper which they already know. It's just not as restrictive and inflexible as paper due to not having a size limitation plus you can incorporate things like video, audio and other files. Other tools are just as restrictive and inflexible because they either follow the same basics or because they have a more complex way of doing things.
Many of the alternatives you speak of come with the same set of restrictions and inflexibility as OneNote. The differences are all in the details plus personal preference. The biggest issue with any of these is that they are reinventing the wheel when it comes to file format. They all use their own proprietary format which means that sharing any data with anybody else 1 to 1 without any compromise requires the other party to use the exact same tool. Now imagine you have students with Windows laptops, Windows tablets, Android tablets, iOS tablets and/or a Mac...the only way to share data with them would be by using OneNote or Evernote because these are available for all mentioned platforms. Or you could use PDF files which anybody can read out of the box with any device right now.
When it comes to handwriting the same can be said. Most apps support it and support it quite well. The biggest problem here is the fact that it is digital and the quirkiness of the device that you use. The Surface Pro and Pro 2 use old Wacom technology which has a big offset, especially in the corners and it lags. That doesn't make handwriting a very pleasant experience. The iPad has the issue that it needs to have a non-Apple bluetooth pen and those are not always a breeze to use. A stylus is almost unusable. It seems that right now the best thing you can do is use the Apple Pencil (hard to get by atm). Do note that palm rejection is also quirky. Most of the times it'll work but sometimes it won't. Since PDF Expert is free app of the week I also highly recommend getting this one. You can pair it with Documents by the same manufacturer so you can use many more file formats (make sure Documents sees PDF Expert, it will activate the advanced PDF options; after that you can delete PDF Expert and just use Documents). The only other good alternative to Documents + PDF Expert that I've seen is GoodReader.