Can't offer a comparison but I'm very happy with Scanner Pro. I like it's ability to sync with MobileMe, as well as email scanned images. It works well, has a nice UI (IMHO) and hasn't crashed out. Works in grey or colour mode and handles multiple pages. My only niggle is that the PDF files it creates are quite large, even in greyscale, but the quality is very good. Even in relatively poor lighting it optimises the image well to produce readable text from the documents.
Oh, and it also works with Dropbox and prints docs from the app using Print n Share
Given it works for me, I've no need (or intention) of trying the other.