Comixology, for its part, has a 17+ age restriction, which means both that a warning is provided when its purchased and access to it can be denied using iOS's built-in restrictions. By comparison, the same issue of Saga in the iBookstore has no ratings at all.
The App Store review process has long been regarded as a capricious gauntlet for developers to run. While its rules are public, they are oftentimes vague and subject to the interpretation of individual reviewers - which may be what happened in the case of Saga - but there is only limited recourse for developers who want to appeal their app's removal.
As a retailer, Apple certainly has the right to choose not to sell material that it finds objectionable. The concern in this case was more that Apple might have been denying a third-party the opportunity to sell content that Apple itself was selling, which proved not to be the case.
Given the concerns about certain content reaching kids, I'd argue that more emphasis should be put on educating parents about iOS's quite effective mechanisms for preventing kids from accessing adult material.
I'm not suggesting that Apple should open the floodgates to pornography and adult content, but it's clear, despite the resolution here, that the App Store review process is badly in need of an overhaul.
In his capacity as Senior Vice President of Internet Software and Services, Apple Exec Eddy Cue oversees the iTunes Store, App Store, and iBookstore, so the ball would seem to be in his court regarding the review process. Content restrictions seem to flow more smoothly on Apple's other storefronts; it's not as if either the iBookstore or iTunes Store shy away from explicit content: You can find Fifty Shades of Grey in the former and plenty of R-rated films for purchase and rent in the latter.
Perhaps the real issue - if you'll pardon the expression - is that content providers feel the need to try and anticipate what will and won't pass muster in the App Store. By putting itself into the role of content gatekeeper, Apple is left in the unfortunate position of being the target for blame when these types of issues arise, even if the company ultimately turns out to be not at fault.
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