I have been using PDFPen for a long time, and just upgraded to PDFPen Pro. Honestly the difference in the feature set between the two is small, but if you need the Pro, then you need it.
I had to put together a 1,000 page pdf in a day, and PDFPen Pro made it easy. My experience is that with many apps, they work until you need them for a large project, and then you find the bugs and the limitations. While I did find a few bugs in PDFPen Pro, they all could be worked around, and I was able to compile about 40 separate documents into a single document, annotate them, create a table of contents, adjust for last minute changes coming in from colleagues, and create a protected pdf really quite easily. I never had to wait for the thumbnails to be drawn (I'm looking at you, Acrobat), and every change was easy and I almost never had to refer to the manual. When I had to completely undo and redo everything (after I changed my mind about some issues), it was very straightforward.
While I didn't use OCR on this project, I use OCR in PDFPen all the time, in both English and Spanish, and mostly it is better than Acrobat's (at least the version that I have). I love the fact that PDFPen will show you the "OCR layer" as a separate item, which makes it much easier to understand what is going on.
I have never liked Acrobat. I keep around the older versions because it seems to just get harder to use in each revision. And, if you have to purchase Acrobat outside of a collection of Adobe apps, the cost is totally beyond belief. And then the learning curve (at least the last version I own, Acrobat X) is very slow.
PDFPen is a welcome addition to my suite of pdf applications. I use Skim for day-to-day reading, because I like its user interface the best of all pdf readers, and I like its way of adding notes to a pdf. I use Acrobat Reader and Preview to make sure that my pdfs display correctly (completely unrelated code in these two apps, so they have different bugs in displaying pdfs). I use Photoshop to convert pdf's to image files, because I like the control it gives me.
And I use PDFPen (and now PDFPen Pro) to edit and compile pdfs.
My only complaint (the 1/2 star deduction) is that PDFPen Pro uses Apple's new document versioning and Save As code. I find this a total time waster, and just a bad idea. But fighting with Apple is like fighting city hall — you aren't going to win, even when they are wrong.