My two cents about why the deeper integration means serious business: handwriting search--every scribble, every handwritten note you take will be OCR'd and you'll be able to hunt them down easily, assuming they're relatively legible and not prescription scribbles from your doctor. From the post:
One of Evernote’s magic features is its ability to make handwriting searchable. We’ve applied this to Penultimate to help you find the notes you’re looking for. Just tap on the new magnifying glass icon in the top right corner of your screen to begin searching your notes. Search results fly in with either a yellow rectangle around the identified words or yellow highlighting in the note title.
One note for users on IOS5--the current version in the app store only works on IOS6. This is a problem for iPad 1 users especially, and we are working on getting Penultimate 4 working for IOS5--that will be available in a future update.