There have been a number of relevant ScanSnap discussions here in the recent past; I’d suggest clicking the Search/spyglass button and checking out some of them.
I used to buy (and update yearly) PDFPen but I found that I preferred the UI and speed of Readdle’s PDF Expert for reading, annotating and signing. A summertime discussion thread about the two apps surfaced a number of other converts from PDFPen. The one disadvantage of PDF Expert is the lack of OCR. Nevertheless, I came to dislike PDFPen’s slowness and clunkiness so much that before getting PDF Expert I used the freeware Skim app - which isn’t bad!