I actually love email. It's great that we have a standard and open protocol for sending and receving virtual mail. Without email we would be now probably using some closed-source proprierary and not interoperable solution witch locks you in. I'm glad it didn't happen.
For hand writing i suggest using Rnote and for normal keyboard writing I suggest Joplin. Keep it synced using cloud provider or using Syncthing for free.
About organizational structure in Rnote I unfortunatelly recommend just saving files in a structure of folders. Rnote is the most polished alternative to hand-writing capabilities of OneNote I've found :c
About importing notes. I don't think that's possible but you can surely export them all to PDF from OneNote. I did that when I migrated.
I’d just like to interject for a moment. What you’re refering to as GNU, is in fact, GNU/Linux, or as I’ve recently taken to calling it, GNU plus Linux. GNU is not an operating system unto itself, but rather a gathering of the GNU corelibs, shell utilities and vital system components that together with a Linux kernel comprise a full OS as defined by POSIX.
Insert meme: Oh, I wouldn't say "freed", more like "under new management" 😅