As has been mentioned, you can attach notes to highlighted text in epub and kepubs. You can't do this for PDFs. I don't ind the keyboard to hard to use, but I have at most put about 20 characters in the note.
Unfortunately, there isn't a good way to get them off the KT. For kepubs, the Kobo desktop application will retrieve them. Put it has no ability to print or extract them elsewhere. For epubs, Calibre has an experimental option to retrieve the notes to the comments field. While this works, I don't find it very practical.
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