Starting to more use bookmarks and thought a long press in the corner could show a list. That could make navigation quite quick for those.
An icon in the same place when toolbar is shown would be handy too. That could mean making it look more like a bookmark. I'm not for borrowing everything from iBooks, but if there isn't an imaginable better way yet, well then.
A drop down for options, like iBooks or PDF Expert, perhaps with tabs also would decrease thumb mouvement and maybe make it clear pressing again in the same place is additional way to close. Looking at more interfaces, saw an Android Nook earlier and some things are slightly interesting.
Edit: When selecting an annotation, buttons for Deep View and search might be handy. And, I'm not sure how Skim does it, perhaps by storing in memory, after an initial search, subsequent are nearly instant. Maybe possible for newer devices. The search window, and perhaps other places with long lists, could use an invisible scrubber, invoked when holding and scrolling the edge. In thousand page works with hundreds of search results, very helpful.
Edit 2: Tried page accessories. Perhaps it could be changed by long pressing the footer and then removed from the ePub menu. Perhaps other things could use the same treatment. I was thinking that maybe like other mid-complexity apps in OS X, it appears or tries to be simple for the typical, but for those that experiment or know how OS X works, there's much hidden but still accessible for those that want it. Such things could also clean up the UI to make what is more frequently used easier and quicker to get to.