I, too, possess an iPad Pro with Apple Pencil, but I opted for the smaller 9.7" one. It was a mistake, the bigger one would have been better, but I love it anyway. for note-taking. It's a godsend to be able to shuffle text around, resize it, undo my errors etc. I wrote something on paper lately and automatically searched for the undo button when I made a mistake and was frustrated when I realized I have to use my eraser.
Anyway, which app are you using for your notes? I'm using OneNote ATM. I can't describe what's missing, I'm just not feeling 100% satisfied.