Just going to give you my point of view.

I used to be a very heavy User of Evernote. I was pretty much digitizing everything. I switched because I really did not like Evernote's editor, I was unsure about their cloud (who are these guys?) and there was some management issues. So I thought MS was a safer choice. I bought a SP4 for that and switched from Mac. Here is for the background.

I had obviously tons of pdfs in Evernote. In this software, what happens is that you just drag and drop the file and you have the pdf displaying. You can also easily manipulate it. It is very convenient and what you would expect. When I switched to Onenote, they just imported the pdf file, that I had to turn into a printout. Every time I wanted to do that, I had to literally print out outside of Onenote. I had to do it hundreds of times! Then when I tried to perform a search, the highlighting was 100% wrong. I also had to download a third-part software to manipulate the pdf. The highlighting issue has been around since 2011 and MS is always claiming they are going to fix it. Since they have not, it means that this is a core issue of the software and not easy to fix at all. It is probably the same issue as the highlighting that does not stick to the text when you move the printout. The conclusion of all this is that Onenote is not good with pdf at all.

I have switched to Windows for this software that is probably the most amazing productivity tool since HyperCard (!). But the overall impression after a few months is that the development is very amateur and that is has been neglected by MS for a while (I hope this is changing). Sometimes, you just wonder if their engineers have ever been using the application. I have a list of issues that are, from my point of view, absolutely unacceptable. MS is claiming that this app can be used by students for manipulating big pdfs... it is just not possible and Evernote is doing most of the time a much better job.

I am waiting for a major release that would solve these issues as I really like the integration with Office for example. In current state, it is not possible to digitize your life on Onenote.