Thanks for the feedback. Note on shared Notes.app notes: use a shared folder. We have 3 kids, my wife and I use a shared Notes.app folder for each kid which is far easier to manage than individual notes.
I think where I’m landing now is that I really want to be able to do my markup in any third party app (PDFExpert, GoodReader) and be able to save directly back into the original note (avoiding an export, edit, re-import loop).
Even more fun would be a note taking app whose native format is PDF. That would solve the problem of what happens when Evernote goes apathetic, or Apple breaks Notes - just move all your notes (PDFs) to the next new tool - no loss of formatting, tags, etc.. GoodReader and PDFExpert are 90% of the way there already - they both just need a decent text editor and syncing.
For now, it looks like I’m going to try living within Apple notes, backfill the 200-300 notes that are WebClipped HTML with Safari “export as PDF” single page PDFs.
— Chris