1) Possibility to ADD SPACE in ink notes. VEEEERY important for people who need to write/draw stuff between lines!
2) More/better hyperlink options. Instead of lots of different notes, I prefer to write long notes. This could be implemented by a TABLE OF CONTENTS, similar to a book's TOC, but of course with good hyperlinking support (similar to PDFs)
3) When you zoom out on a long note with many pages, you should get an overview of all the pages, from which you can easily navigate to any page.
BTW I just watched some demo videos of the HTC Flyer with some version of Evernote (?). AWESOME!!! I'm a bit skeptical of the palm rejection system... maybe that's why the tablet is so small?