The App Store has always been Apple's playground -- you get to play there if you adhere to the rules. Sometimes the rules are straight forward; other times the rules are malleable and determined by Apple on a seemingly case-by-case basis. The latest rejection controversy involving Autriv and its SignMyPad app definitely falls into the latter scenario.
SignMyPad was recently updated to version 5 and added iCloud so users could sync their PDF files across iOS devices. Apple rejected this latest version because it will not allow iOS applications to use iCloud to sync "non-user-generated" data between devices. Even though the app adds a signature to a document and saves it as a new file, Apple does not consider this to be user-generated content. The developers pleaded their case with Apple, and the company would not budge. Apple's answer to the team was to drop iCloud and use a third-party service instead.
Though it seems unreasonable to push developers away from its own service, there may be justification for Apple's rejection that lay outside this "user-generated" clause. First, iCloud is a limited resource that users have to pay to use. Yes, you get 5 GB of free storage space, but your allotment could quickly fill up with beefy PDF files uploaded by single-purpose apps like SignMyPad that add only a signature to the document. One little signature on a handful of these documents, and a user is calling Apple to complain that their iCloud storage is full. They don't understand why they are maxed out because they only added a signature, how could that take up so much space?
Other apps like PDFpen use iCloud, but PDFPen is a full-scale editor that lets you annotate, correct and sign PDF files. Apple may be looking at an app like PDFpen and giving it the thumbs up because of its broad editing capabilities, while rejecting SignMyPad because it only adds a signature. This signature is apparently not significant enough to be considered user-generated content by Apple. Plus, iCloud has been experiencing significant growing pains since it launched, and there are other services like Dropbox or even email that are better equipped to share large files.