One thing with the native software that I'd like to see, and which seems a rather trivial thing to add, is a left-handed option for when one opens a notes page while displaying a PDF document. Right now the document is on the left, and the notes page is on the right; this is perfect for right-handed people, but for me, trying to write on the right means my hand will cover the PDF document, and sometimes will be detected and do something unexpected.
This feature has the potential to be very useful; right now it's very difficult to use for about 15% of users (according to stats I've read) - and 100% of those in my home.
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