I've tried using Goodnotes 5 and although it is way better for taking notes and has great search features and handwriting indexing built in, from a workflow point of view I found it too cumbersome moving each note into EN. What would be great would be if I could automate the moving of notes from GN to EN.
SO - I"ve been using Penultimate, which automatically puts my handwritten notes (on iPad) into EN and makes them searchable. Penultimate is not as good as GN but good enough.
I also use paper and pen - have been using Whitelines notebooks and Whitelines Link - process is cumbersome but works well. I"ve also been playing with using the camera feature in EN notes to add handwritten notes, that might end up being the best option.