MFi controller support seemed like a great compromise: gamers who wanted real game controls would be able to get devices that worked. And the fact that support was built in to the operating system meant broad support. Or so I thought. Five months after iOS 7's release, there's still only a relative handful of games that make use of MFi game controllers. Not to mention a paucity of MFi controllers.
Well I think it's a combination of Apple not promoting it and developers not adding support to their apps. I think Apple needed a popular app to add controller support plus the controller to come out when iOS 7 launched for it to take off. To me it seems like Apple added it as a last minute feature. I think it has huge potential. Just imagine playing a game with a controller but the game is being airplay mirrored to an Apple TV.
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Certainly a feature that has a lot of potential but as you stated in the article, controllers are more expensive than real console controllers. That's something that must change if the feature is going to really catch on with developers