The ability to create folders and sub-folders is definitely feature number one I would like to see.
I do not know if this can be done through a software update, but the highlighting needs to be improved. I can see this being very useful to students and scholars. However, it is very cumbersome to mark up pages. If it were easier, the highlighting would far surpass highlighting a physical book. I would be able to quickly go to highlights and notes, rather than either keeping a log of them separately, or flipping pages.
In the grand scheme of ebooks, however, scholars are a small, probably less profitable market, so I am not holding my breath. Right now I rarely use the highlight feature and simply keep a log with notes.
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