When in "normal" handwriting mode the same scolling (manual and automatic) mechanisms could be offered, regardless in which magnification. That would give more flexibility and avoids need to switch between view modes if using different tools (e.g. Line tool, handwriting tool).
I am often switching between notbooks and comparing for example similiar documents. Currently it is hard to keep track in which document I'm currently in. My suggestion would be to show the name of th selected notebook for example as non-printed watermark on top of the page or at the bottom.
There is no reason why the notebook list should be at the top of the list because most times you will be using accessing notes and not remote data.
Currently it seems the external keyboard is a bit flakey (Especially you can't access some of the text box features while you are using it since you can't see the text toolbar).
When you make a selection using the pointer tool and then do reset zoom it should zoom to fit the selection.
There needs to be a better way of indicating what the current zoom level is (Currently there is no indication so anything will be better).
The dialog where you rotate an image should have a field that lets you both see and specify the degrees to rotate with.
When you export to Omnipage the link back into the notebook should also go to the specific page.
It makes more sense to have the tools at the top instead of at the bottom in the iPhone user interface
There should be an option to also show the URL on top of a web clipping (Instead of right now when you have to clip the configure button panel).
Add the option to tie audio recordings to a notebook instead of a page so that it can continue to record when you change pages.
When I write something outside the default page size (outside of the dotted lines that appear when you zoom out), the default zoom comprises my whole drawing. That's perfect.
But when I remove the drawings outside of the default page size, the default zoom doesn't return to the default page, but still shows the (now empty) area outside the page.