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).
The dialog where you rotate an image should have a field that lets you both see and specify the degrees to rotate with.
It makes more sense to have the tools at the top instead of at the bottom in the iPhone user interface
If you do a long press in the document the insert menu should show up.
Make it possible to use the manual wrist guard inside the magnified zoom area so that you can drag it in from either top top or the bottom of the magnified zoom area and be able to wrest your hand on it.
Would be nice to be able to have a calendar view of the notebook list so that Notify could more easily be used as a journal.
Would be nice to get some more statistical information about the contents of a note for instance word, character and paragraph count.
Currently you can only search the contents of all your notes. Would be useful to be able to search individual notes too.
Add an ability to somehow specify how large the auto advance window should be in the mirrored view so that you can get the text to advance further or shorter.
As a leftie, that would be VERY useful.
Add an option to move the remote services back to the top of the notebook list as it was before version 4.0.
The same option could also affect the insert document window.