I agree with you Robert, Kobo's annotation ability (lack of) is one of its major downfalls, and like you, I've had to develop my own "system" to make up for Kobo's limitations.

My system is actually pretty simple: I highlight text on my Kobo, and take corresponding notes in my pocket Moleskine. After finishing the book, I transfer my highlights (using Kobo Utilities) and type up my notes into Evernote.

Does the screenshot hack work on the Aura?