You can count me as one of the (apparently few) people who think that the new interface is an improvement. I really like being able to hold my iPad mini in portrait orientation and using the zoom area to write in. I also like the fact that new pages appear naturally as I advance the zoom area (I really hated having to zoom out to add a page and then having to zoom back in).
I have noticed that the zoom box jumps into the top left corner of the screen occasionally and assume that this will get fixed in the near future -- this is mostly an annoyance and the kind of thing that can be expected when anyone makes this big of a change to an application.
The more frustrating thing is that I just lost an hour of note taking. Somehow, penultimate managed to sync the background for my notes (two pages), but my notes are nowhere to be seen. They don't show up on my iPad and they don't show up on the desktop or the web..... very frustrating. This happened to me with an earlier version, so it's not specific to the new release, but it is the kind of thing that would cause me to move away from Evernote entirely (and I am a paying customer).
As much as I like the new version, I have a couple of suggested improvements 1) make it possible to use zooming without scrolling -- writing on a scrolling screen really is unnatural and there are lots of examples of how to advance the zoom window more effectively; 2) I'm surprised by the poor quality of the "ink" in this version of Penultimate -- this used to be the killer feature of Penultimate, now the ink is really pretty pathetic, especially when compared to ether apps.
Why do I continue to use Penultimate when there are clearly better note taking apps -- some of which actually synchronize with Evernote? Simple, the seamless integration/synchronization with Evernote. Hopefully, Penultimate will continue to provide updates in the coming weeks to address the issues that I and others have raised and I won't have to find an alternative. The fact that Penultimate took this big of a step after such a long time with an outdated interface is promising.