Make the application more responsive while drawing, scrolling & zooming.
Right now it is fairly sluggish to scroll around the UI and every once in a while a stroke is completely missed while doing quick hand writing.
Right now it is quite often that the application unexpectedly crashes.
I have determine that in most cases this is because the application runs out of working memory so improve the memory usage of the application during normal use.
Allow syncing of notes to Dropbox & Box.net accounts.
Also allow choosing what format to sync in (Including native format).
Specifically WebDAV and FTP would be nice to access from within the application.
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.
The scrolling while in the zoom mode could be smarter in that it would be nice if you saw a faded preview of the left side as you get close to it on the right side so that when the view scrolls automatically you already know where it will scroll to.
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).
Password protection needs to be added both as a setting for the entire application and something that can be added to specific notes.
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).